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- EMDB-29495: 40S subunit of the Giardia lamblia 80S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-29495
Title40S subunit of the Giardia lamblia 80S ribosome
Map dataMain map for building the body of the 40S subunit.
Sample
  • Complex: 60S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome
    • RNA: x 2 types
    • Protein or peptide: x 32 types
  • Ligand: x 4 types
KeywordsGiardia lamblia / Ribosome structure / Translation / parasite / RIBOSOME
Function / homology
Function and homology information


endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e ...Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S4e, N-terminal, conserved site / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S19e / 40S Ribosomal protein S10 / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / S27a-like superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Beta-grasp domain superfamily / Ribosomal protein S25 / S25 ribosomal protein / RS4NT (NUC023) domain / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal family S4e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal protein S28e conserved site / Ribosomal S3Ae family / Ribosomal protein S28e signature. / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S14/S29 / 50S ribosomal protein L30e-like / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S10 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / K homology domain superfamily, prokaryotic type
Similarity search - Domain/homology
40S ribosomal protein S30 / 40S ribosomal protein S8 / 40S ribosomal protein S21 / Ribosomal protein S28 / Ribosomal protein S20 / Ribosomal protein S24 / 40S ribosomal protein S6 / Ribosomal protein S29A / 40S ribosomal protein S25 / 40S ribosomal protein S3 ...40S ribosomal protein S30 / 40S ribosomal protein S8 / 40S ribosomal protein S21 / Ribosomal protein S28 / Ribosomal protein S20 / Ribosomal protein S24 / 40S ribosomal protein S6 / Ribosomal protein S29A / 40S ribosomal protein S25 / 40S ribosomal protein S3 / Ribosomal protein S15 / Ribosomal protein S13 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S4 / Ribosomal protein S27 / Ribosomal protein S16 / Ribosomal protein S9 / Ribosomal protein S2 / Ribosomal protein S27a / 40S ribosomal protein S26 / Ribosomal protein S17 / Ribosomal protein S10B / Small ribosomal subunit protein eS1 / Ribosomal protein S12 / Ribosomal protein S18 / Ribosomal protein S14 / SSU ribosomal protein S7P / SSU ribosomal protein S12P / 40S ribosomal protein S7 / SSU ribosomal protein S19E / SSU ribosomal protein S17P / SSU ribosomal protein S8P
Similarity search - Component
Biological speciesGiardia intestinalis assemblage A (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsEiler DR / Wimberly BT / Bilodeau DY / Rissland OS / Kieft JS
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118070 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI149210 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128680 United States
CitationJournal: Structure / Year: 2024
Title: The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function.
Authors: Daniel R Eiler / Brian T Wimberly / Danielle Y Bilodeau / J Matthew Taliaferro / Philip Reigan / Olivia S Rissland / Jeffrey S Kieft /
Abstract: Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure ...Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure of the G. lamblia 80S ribosome bound to tRNA, mRNA, and the antibiotic emetine by cryo-electron microscopy, to an overall resolution of 2.49 Å. The structure reveals rapidly evolving protein and nucleotide regions, differences in the peptide exit tunnel, and likely altered ribosome quality control pathways. Examination of translation initiation factor binding sites suggests these interactions are conserved despite a divergent initiation mechanism. Highlighting the potential of G. lamblia to resolve conserved biological principles; our structure reveals the interactions of the translation inhibitor emetine with the ribosome and mRNA, thus providing insight into the mechanism of action for this widely used antibiotic. Our work defines key questions in G. lamblia and motivates future experiments to explore the diversity of eukaryotic gene regulation.
History
DepositionJan 20, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29495.png

Downloads & links

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Map

FileDownload / File: emd_29495.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map for building the body of the 40S subunit.
Voxel sizeX=Y=Z: 0.8211 Å
Density
Contour LevelBy AUTHOR: 0.0895
Minimum - Maximum-1.459785 - 3.9904838
Average (Standard dev.)-0.0012536786 (±0.15223372)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 369.495 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Main map for building the head of the 40S subunit.

Fileemd_29495_additional_1.map
AnnotationMain map for building the head of the 40S subunit.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Main map for refinement of the 40S subunit.

Fileemd_29495_additional_2.map
AnnotationMain map for refinement of the 40S subunit.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of focused refinement P191 J466 Focused Head 2p94.mrc

Fileemd_29495_half_map_1.map
AnnotationHalf map of focused refinement P191_J466_Focused_Head_2p94.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of focused refinement P191 J466 Focused Head 2p94.mrc

Fileemd_29495_half_map_2.map
AnnotationHalf map of focused refinement P191_J466_Focused_Head_2p94.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 60S ribosomal subunit of the 80S Giardia intestinalis assemblage ...

EntireName: 60S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome
Components
  • Complex: 60S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome
    • RNA: 18S rRNA18S ribosomal RNA
    • Protein or peptide: 40S ribosomal protein SA
    • Protein or peptide: 40S ribosomal protein S3a
    • Protein or peptide: Ribosomal protein S2
    • Protein or peptide: Ribosomal protein S3
    • Protein or peptide: 40S ribosomal protein S4
    • Protein or peptide: SSU ribosomal protein S7P (Fragment)
    • Protein or peptide: 40S ribosomal protein S6
    • Protein or peptide: 40S ribosomal protein S7
    • Protein or peptide: 40S ribosomal protein S8
    • Protein or peptide: Ribosomal protein S9
    • Protein or peptide: Ribosomal protein S10BRibosome
    • Protein or peptide: SSU ribosomal protein S17P
    • Protein or peptide: Ribosomal protein S13
    • Protein or peptide: Ribosomal protein S14
    • Protein or peptide: Ribosomal protein S15
    • Protein or peptide: Ribosomal protein S16
    • Protein or peptide: Ribosomal protein S17
    • Protein or peptide: Ribosomal protein S18
    • Protein or peptide: SSU ribosomal protein S19E (Fragment)
    • Protein or peptide: Ribosomal protein S20
    • Protein or peptide: 40S ribosomal protein S21
    • Protein or peptide: SSU ribosomal protein S8P (Fragment)
    • Protein or peptide: SSU ribosomal protein S12P
    • Protein or peptide: Ribosomal protein S24
    • Protein or peptide: 40S ribosomal protein S25
    • Protein or peptide: 40S ribosomal protein S26
    • Protein or peptide: Ribosomal protein S27
    • Protein or peptide: Ribosomal protein S28
    • Protein or peptide: Ribosomal protein S29ARibosome
    • Protein or peptide: Ribosomal protein S27aRibosome
    • RNA: tRNATransfer RNA
    • Protein or peptide: Ribosomal protein S12
    • Protein or peptide: 40S ribosomal protein S30
  • Ligand: MAGNESIUM ION
  • Ligand: emetine
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: 60S ribosomal subunit of the 80S Giardia intestinalis assemblage ...

SupramoleculeName: 60S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#34
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)

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Macromolecule #1: 18S rRNA

MacromoleculeName: 18S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 470.516812 KDa
SequenceString: CAUCCGGUCG AUCCUGCCGG AGCGCGACGC UCUCCCCAAG GACGAAGCCA UGCAUGCCCG CUCACCCGGG ACGCGGCGGA CGGCUCAGG ACAACGGUUG CACCCCCCGC GGCGGUCCCU GCUAGCCGGA CACCGCUGGC AACCCGGCGC CAAGACGUGC G CGCAAGGG ...String:
CAUCCGGUCG AUCCUGCCGG AGCGCGACGC UCUCCCCAAG GACGAAGCCA UGCAUGCCCG CUCACCCGGG ACGCGGCGGA CGGCUCAGG ACAACGGUUG CACCCCCCGC GGCGGUCCCU GCUAGCCGGA CACCGCUGGC AACCCGGCGC CAAGACGUGC G CGCAAGGG CGGGCGCCCG CGGGCGAGCA GCGUGACGCA GCGACGGCCC GCCCGGGCUU CCGGGGCAUC ACCCGGUCGG CG CGGUCGC GGCGCGCCGA GGGCCCGACG CCUGGCGGAG AAUCAGGGUU CGACUCCGGA GAGCGGGCCU GCGAGACGGC CCG CACAUC CAAGGACGGC AGCAGGCGCG GAACUUGCCC AAUGCGCGGC GCGCGAGGCA GCGACGGGGA GCGCGCGAGC GAGG CGGGC CCACAGCCCC CGCCGCGGAG CCGAGGGCAA GGUCUGGUGC CAGCAGCCGC GGUAAUUCCA GCUCGGCGAG CGUCG CGCG GCGCUGCUGC AGUUGAAACG CCCGUAGUUG GCCCCCCGCC GCCACGAGGA AACGGGAGCG CUCCAGGCAG GCCCGU UGG ACCCGCCGCG UGGGACCGCG CAGCGGGCGC GGCGCGCCGC GGCAGCCCCG AGGAGAGCGG GCGGGGGCAC CGGUACC GG CCGGGGACGG GUGAAACAGG AUGAUCCCGC CGAGACCGCC GGCCGCGCAG GCGCCUGCCA AGACCGCCUC UGUCAAUC A AGGGCGAAGG CCGGGGGCUA GAAGGCGAUC AGACACCACC GUAUUCCCGG CCGUAAACGG UGCCGCCCCG CGGCCGGCG CGCGCGUCCC GCCGGCCGCC CAGGGAAACC GGGAGGCUCC GGGCUCUGGG GGGAGUAUGG CCGCAAGGCU GAAACUUGAA GGCAUUGAC GGAGGGGUAC CACCAGACGU GGAGUCUGCG GCUCAAUCUG ACCCAACGCG CGCACCUCAC CAGGCCCGGA C GCGCGGAG GACCGACAGC CGGGCGCGCU UUCGCGAUCG CGCGGGCGGU GGUGCAUGGC CGCUCCCAGC CCGUGGCGCG AG CCGUCUG CUCCAUUGCG ACAACGAGCG AGACCCCGGC CGCGGGCGCC GCGGGACGGC CCGCGCGAGC GGGAGGACGG CGG GGCGAU AGCAGGUCUG UGAUGCCCUC AGACGCCCUG GGCCGCACGC GCGCUACACU GGCGGGGCCA GCCGGCGCCC GCGA GGACG CGCGGAGCCC CCGCCGUGGC CGGGACCGCG GGCUGGAACG CCCCCGCGCA CCAGGAAUGU CUUGUAGGCG CCCGC CCCC ACCGCGCGCC GGACGCGUCC CUGCCCCUUG UACACACCGC CCGUCGCUCC UACCGACUGG GCGCGGCGGC GAGCGC CCC GGACGCGCGA AGGGCCGCGA GCCCCCGCGC CUGGAGGAAG GAGAAGUCGU AACAAGGUAU CCGUAGGUGA ACCUGCG GA UGGAUCCCU

GENBANK: GENBANK: CP110916.1

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Macromolecule #32: tRNA

MacromoleculeName: tRNA / type: rna / ID: 32 / Number of copies: 1
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 23.749051 KDa
SequenceString:
GGGUAAUUGG CGCAGUUGGU UAGCGCGCGG GUCUCAUAAU CCCGAGCUCG UGAGUUCGAU CCGCACAUUC CCCA

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Macromolecule #2: 40S ribosomal protein SA

MacromoleculeName: 40S ribosomal protein SA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 28.101803 KDa
SequenceString: MSTEKTSQAS KEYQLKEADV KKMLVATTHL GVRNIDRRMQ FYIFDRQKDG TFVFNLQKVW AKIVFAARIL VTIDDPAEIA VVANRPDAQ RAILKFCKYT HATAFPGRFI PGNFTNRMNP NYCEPRLLLV NDPVVDRQAI LEASYVNIPT ISLCNSDANL K FIDVAIPC ...String:
MSTEKTSQAS KEYQLKEADV KKMLVATTHL GVRNIDRRMQ FYIFDRQKDG TFVFNLQKVW AKIVFAARIL VTIDDPAEIA VVANRPDAQ RAILKFCKYT HATAFPGRFI PGNFTNRMNP NYCEPRLLLV NDPVVDRQAI LEASYVNIPT ISLCNSDANL K FIDVAIPC NNKTPMSIGL IYWLLAREVL RLKGSISRTE EWDVKPDLFV ALPEEIPDEE ESEDFYDDDE EEDEEFSAGN GN LFDEY

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #3: 40S ribosomal protein S3a

MacromoleculeName: 40S ribosomal protein S3a / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 28.413148 KDa
SequenceString: MAIGGNKTGK KKITQRKNPD PYLKKEWYPV IAPAHFKSRH IGQTPVTKTA GLRVATDVIN HRVYEVNLGD LNPGAEDLNG NTKFYLQTQ LVSDGKCLTN FHGMDITRHK YGSLFRKGCD CIDVFMDIPT TDGYLLRVFV IAFTDRFRFQ RRKNCHVKGR V IRMMRAGI ...String:
MAIGGNKTGK KKITQRKNPD PYLKKEWYPV IAPAHFKSRH IGQTPVTKTA GLRVATDVIN HRVYEVNLGD LNPGAEDLNG NTKFYLQTQ LVSDGKCLTN FHGMDITRHK YGSLFRKGCD CIDVFMDIPT TDGYLLRVFV IAFTDRFRFQ RRKNCHVKGR V IRMMRAGI YETLHNELGK VSIPVLVTKL SNFEVNAKLT EALQKITMCR DVMIRRVKVV KRPRNTMELL STMHDSNQVR NL AEGQSIQ Q

UniProtKB: Small ribosomal subunit protein eS1

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Macromolecule #4: Ribosomal protein S2

MacromoleculeName: Ribosomal protein S2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 26.765695 KDa
SequenceString: MQAESAPRPE RPERGERGPR QMEEEEWHPS TKLGRLVKAG KIESLYDIFK YSLPIKETEI IDYFFPKSEL AEEVCNIMSV QKQTTAGQR TRFRAHVIVG NRDGFIGYGA GVSKEVANAI KKAAKNARLN IVPVRRGFWG GKLGDPHTVS SKLSGKCGSV R VRLIPAPR ...String:
MQAESAPRPE RPERGERGPR QMEEEEWHPS TKLGRLVKAG KIESLYDIFK YSLPIKETEI IDYFFPKSEL AEEVCNIMSV QKQTTAGQR TRFRAHVIVG NRDGFIGYGA GVSKEVANAI KKAAKNARLN IVPVRRGFWG GKLGDPHTVS SKLSGKCGSV R VRLIPAPR GAGIVASPTV AKVLEFAGVS DVFTRQSGHS RTLMNSVGAV YNALKSSYSI LTPDLWKKEQ LDHVQDIRTM SL AD

UniProtKB: Ribosomal protein S2

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Macromolecule #5: Ribosomal protein S3

MacromoleculeName: Ribosomal protein S3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 24.779148 KDa
SequenceString: MPRIVRRDEE NVYYSKYLND CIMEAELHEF FSRELVDAGY ASCSLCRTID SICVIIQCAE PEVVMGDNHY RLHKIEYLLA GRFMCDPKN FNIWVDKIIK RGLSAEIMVD NLRAKLEEAM PIRRAAYSII RTAMRAGAAG CEVIVAGKLR AQRARANKFK E GCLISTGH ...String:
MPRIVRRDEE NVYYSKYLND CIMEAELHEF FSRELVDAGY ASCSLCRTID SICVIIQCAE PEVVMGDNHY RLHKIEYLLA GRFMCDPKN FNIWVDKIIK RGLSAEIMVD NLRAKLEEAM PIRRAAYSII RTAMRAGAAG CEVIVAGKLR AQRARANKFK E GCLISTGH PKRIFLAEAT RHIKMRQGVI GVKVRIYNPN IRGAVMPDKI EIGAFSRQK

UniProtKB: 40S ribosomal protein S3

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Macromolecule #6: 40S ribosomal protein S4

MacromoleculeName: 40S ribosomal protein S4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 30.464781 KDa
SequenceString: MARGVRKHLK RLNAPKHWLL DKMGGIWAPR PTNGPHGLRE CIPLILILRN RLHYANTYAE TSMILQDKNV LIDGKPRTDP TFPVGFMDV FEIPKVHKTF RVLYDVKGRF TLVPIQSNEA GFKLCRVQKI FLGDKGMPYL STHDARTIRF PHPDIKTNDT I KINLKTGK ...String:
MARGVRKHLK RLNAPKHWLL DKMGGIWAPR PTNGPHGLRE CIPLILILRN RLHYANTYAE TSMILQDKNV LIDGKPRTDP TFPVGFMDV FEIPKVHKTF RVLYDVKGRF TLVPIQSNEA GFKLCRVQKI FLGDKGMPYL STHDARTIRF PHPDIKTNDT I KINLKTGK IDEWYKFDIG KIVMVTGGRN CGRIGTIQAI DKHMGSYTMI RMKDTEGTEF LTRLCNVFVI GNDSPAVAIP TT KGIRPDI IKNRELRLRS IAKRGGGASY E

UniProtKB: 40S ribosomal protein S4

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Macromolecule #7: SSU ribosomal protein S7P (Fragment)

MacromoleculeName: SSU ribosomal protein S7P (Fragment) / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 21.058275 KDa
SequenceString:
MSLEVALFNK WPLTDVKCQD ESLEAYISID NHSFVPHSAG RWSAKRFRKA KCPVVERLTN SLMMHGRNSG KKLMAMKTVG EAFELINLY TGKNPVQVLV DAVANSGPRE DSCRIGKGGQ VRRQSVDVSP LRRVNIGIYN IATGARKAAF RKVRPFAECL A EEIMNAAA GADKSYAISQ RNSVERIAVS NR

UniProtKB: SSU ribosomal protein S7P

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Macromolecule #8: 40S ribosomal protein S6

MacromoleculeName: 40S ribosomal protein S6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 28.084123 KDa
SequenceString: MPKGSFCKVN ISNPVTGANK SLMIEDFRKS QTIHGLRMAS EFDGAALGEE YAGCTFRITG GNDAQGFPMY QGVLKSQRAR LLLRQGAKC YLHRRNGERK RKSIRGCIVG PDLHALSVVL VDAGDKTLPG LTDVVVPKRL VPKRASKIRR LFGLPTTKVD P KDQMLVCE ...String:
MPKGSFCKVN ISNPVTGANK SLMIEDFRKS QTIHGLRMAS EFDGAALGEE YAGCTFRITG GNDAQGFPMY QGVLKSQRAR LLLRQGAKC YLHRRNGERK RKSIRGCIVG PDLHALSVVL VDAGDKTLPG LTDVVVPKRL VPKRASKIRR LFGLPTTKVD P KDQMLVCE LIKELGHEVT LKNGEKKLKY PKVQRVVTDE KYARKQRVIA EKKEIMRKSL QQLEEYKALL SRMGKQHNIR IY KPAKRTV E

UniProtKB: 40S ribosomal protein S6

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Macromolecule #9: 40S ribosomal protein S7

MacromoleculeName: 40S ribosomal protein S7 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 23.072963 KDa
SequenceString: MNFHLTRSIP SMTFPAQRKI RKPFEKLSEL EKQVAGTLLK LEDDPDLREM GLGTLYISSV KEIAVDGDKK AAVVYVPYPM LQSFQKNSE ALILKLEKNH SGHRFIIVAN RTIMKNAYVF TGKKSIRRPR SRTMTSVYNC ILDDICYPIH VIGKRTLYPA G SNPRLQVV ...String:
MNFHLTRSIP SMTFPAQRKI RKPFEKLSEL EKQVAGTLLK LEDDPDLREM GLGTLYISSV KEIAVDGDKK AAVVYVPYPM LQSFQKNSE ALILKLEKNH SGHRFIIVAN RTIMKNAYVF TGKKSIRRPR SRTMTSVYNC ILDDICYPIH VIGKRTLYPA G SNPRLQVV LPKAVYNEVS ERTKTYSAVY KALTERDTEF IFM

UniProtKB: 40S ribosomal protein S7

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Macromolecule #10: 40S ribosomal protein S8

MacromoleculeName: 40S ribosomal protein S8 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 19.451555 KDa
SequenceString:
MGITHDKMYK RSKTGAVQGK WHKKRKYNLG RQPANTKLIV KVTSKKNEGQ KISTIRCRGG NIKRRALRLS HGSFAWGSAD ISHKARILQ VVYNSTSNEL VRTNTLVKGC VVQIDSAPFK SALSNDTLDK EILDQIRGDH ILARISSRPG QVGTADGYIL E GPELLFYQ KKLAPK

UniProtKB: 40S ribosomal protein S8

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Macromolecule #11: Ribosomal protein S9

MacromoleculeName: Ribosomal protein S9 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 21.699322 KDa
SequenceString:
MPRISRHRNS SKTYSTPKKP FTKPRLDAEL KLCGEYGLKC KREIYRARYM LAKIRRTARN LLTLDENDIK RRFEGAALLR RLHMLGILD EEKDQLDYVL GLRIEDIFKR RLQSVIVESK LAKSVHHARN MIKARHISVG GQIVNIPSYM VRISNTSRVA I ADTSSLAP NGKPGRTKRA AARRQSSGDN E

UniProtKB: Ribosomal protein S9

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Macromolecule #12: Ribosomal protein S10B

MacromoleculeName: Ribosomal protein S10B / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 15.406633 KDa
SequenceString:
MVHIPKAVYK AVYAHLYENA SLALKEYWRV GNVPGITYVD ENGKLCNPTY LHVNCIMQSL ESRGVVKDTF AWRHHYYLLT EKGEQFIRK ELDLTDDVLP TPYSKPSIKP PQYAQCFSSK GKPDRAPQPK PDEAK

UniProtKB: Ribosomal protein S10B

+
Macromolecule #13: SSU ribosomal protein S17P

MacromoleculeName: SSU ribosomal protein S17P / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 23.160898 KDa
SequenceString: MSATKDKQQS NAGAKVGGRH PLRPDPDRER RALERAETLR KAAYEMAENQ HERAYHKQSQ IFQGRFLRKD NARCLRFYKS IGMGYHTPI TAINGTYIDK KCPFTGNVSI RGRILRGVVH SAKMQRSIIV RRDYLHFVQK YKRYERRHKH VAAHLSPCFR V KEGDIVTI ...String:
MSATKDKQQS NAGAKVGGRH PLRPDPDRER RALERAETLR KAAYEMAENQ HERAYHKQSQ IFQGRFLRKD NARCLRFYKS IGMGYHTPI TAINGTYIDK KCPFTGNVSI RGRILRGVVH SAKMQRSIIV RRDYLHFVQK YKRYERRHKH VAAHLSPCFR V KEGDIVTI GECRPLSKTI RFNVIKVEPV SEAAKKRFSP F

UniProtKB: SSU ribosomal protein S17P

+
Macromolecule #14: Ribosomal protein S13

MacromoleculeName: Ribosomal protein S13 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 17.627873 KDa
SequenceString:
MGRMHSKGKG ISRSAIPYTR APAPWNKYTP EDVCEQICKL AKKGTPPSRI GLILRDQFAI GQVKNVTGSK IVRILKAKGL APEIPEDLY CMIKKAVAIR KHLERSRRDK DSKFRLILVE SRIHRLARYY RQARRLPPTF RYKSDQAAAL LATYA

UniProtKB: Ribosomal protein S13

+
Macromolecule #15: Ribosomal protein S14

MacromoleculeName: Ribosomal protein S14 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 15.755995 KDa
SequenceString:
MSRKVTYAPE NLPAKNNNSE AFAVCHIYAG KNDTFIHVTD LSGRETIGRV SGGMKVKRHC DEPSAYAAMQ ATQDLIEIIT DRGITAVHI KIRADGGTGK RVYGQGGSAA IRALVRGGIK IGRIEDSTPI PTDRTRHKGG RRGRRL

UniProtKB: Ribosomal protein S14

+
Macromolecule #16: Ribosomal protein S15

MacromoleculeName: Ribosomal protein S15 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 16.728102 KDa
SequenceString:
MTDQVKTRRR GLAQPNFRGV EVEKLATMKI TDILPKLNAR CRRRIGKHGL SMKHLRFVNK LRLRRAAQPS QKPKIVRTHL RDMIIFPEM IGMTVSVYNG RQFIPVEIKP PMVGRALREY SMSYKIVSHG KVGIGATRSS KFVPLR

UniProtKB: Ribosomal protein S15

+
Macromolecule #17: Ribosomal protein S16

MacromoleculeName: Ribosomal protein S16 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 17.634584 KDa
SequenceString:
MAKGNRRDLL ERNDIEVRER DKYTVHTLGK KKNSVAVAFV KAGKGDILVN NVPLALVRPE ILRTKVSEPI MILGESLFKG LDMNIKVAG GGHVSQIYAV RQAISRGVLA SVKDEAARSE LRAKLVSYDR QLVVSDPRRC EAKKFGGRGA RARRQKSYR

UniProtKB: Ribosomal protein S16

+
Macromolecule #18: Ribosomal protein S17

MacromoleculeName: Ribosomal protein S17 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 15.757351 KDa
SequenceString:
MGKVRTKTIK RAARKIVENN YESLKPKDFQ NNKAICSKRN VAIIPSKRLR NKVAGYVTTL MNRVVKGPVH GISLRLQEEE RERRDNYAP KKSEFDVENI TVSGATQQMI DSIGFKCMST SLKVIDPTMR KRARDTRE

UniProtKB: Ribosomal protein S17

+
Macromolecule #19: Ribosomal protein S18

MacromoleculeName: Ribosomal protein S18 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 17.510338 KDa
SequenceString:
MTTIVQPNDY RDLLRMFNTN IQGKVVLECA LVGIKGIGRR FANVALKKAN IDVHKRAGEL TAAEEDALMK VLEDPLSHGI PAWMLNRNN DFESGKDMHI LVNTIASTHR ADLERLRKTR CERGVRHHHN LKVRGQHTKS TGRRGHVVGV QRKKK

UniProtKB: Ribosomal protein S18

+
Macromolecule #20: SSU ribosomal protein S19E (Fragment)

MacromoleculeName: SSU ribosomal protein S19E (Fragment) / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 17.816758 KDa
SequenceString:
VRQRIHIKLK YWSINQLLGM SSVTRVPADV FINSFAAHLK NRGIIKCPAF TDYVKTGVSR QYAPRDADWF YIKAASVIRH FYISGSHSI GVAGLARKYS SLQKGKTTPH HTKRASCKVI RSIVSQFLGQ KLLIAGERGR HISPNGRKMV EDFAEGLQK

UniProtKB: SSU ribosomal protein S19E

+
Macromolecule #21: Ribosomal protein S20

MacromoleculeName: Ribosomal protein S20 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 14.073192 KDa
SequenceString:
MAESVSTGGV NLADHKDGKD MHQKYTIIVV GKDLKLVERY VKSIVKEGRA FGISGPCRAP VRRLTITTRK SPCGEGTNTW HRFELRMYK RTFWVTCGGN DISTILSKTV VIPGIQVTVE VEEPDNE

UniProtKB: Ribosomal protein S20

+
Macromolecule #22: 40S ribosomal protein S21

MacromoleculeName: 40S ribosomal protein S21 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 9.686149 KDa
SequenceString:
MQSDDIGMKN SSGVVVDAYI PRKCSATNRL IGPKDHAAVQ LSVARVNDKG KMIENNYVTF AFCGAIRSRG GVDSAFMLLA QEHGLMERL

UniProtKB: 40S ribosomal protein S21

+
Macromolecule #23: SSU ribosomal protein S8P (Fragment)

MacromoleculeName: SSU ribosomal protein S8P (Fragment) / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 14.770346 KDa
SequenceString:
MVRINVLRDA LKSICNAQRI GKKQVIVRPS SKVIIEFLQL MQKNGYISDF AVVDNHRSNR IVVNLIGRLN KAGVISPRFD IPANDIEKW VVNLLPSRLF GHIILTTSQG IMDHIEAQHR QIGGKVIGYF Y

UniProtKB: SSU ribosomal protein S8P

+
Macromolecule #24: SSU ribosomal protein S12P

MacromoleculeName: SSU ribosomal protein S12P / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 15.89784 KDa
SequenceString:
MSKTSGLYTA RKLRTVRRVN RWADKKYRKA HLGTWLKANP LEGACMARGI VTQKIGISAK QPNSAVRKAV RVQLTKNSKK ITAFVPRDG SITYIDNNDE VLVAGFGRAG RAVGDIPGCR FKVIKVAGIG LLALFLRKRE KRAR

UniProtKB: SSU ribosomal protein S12P

+
Macromolecule #25: Ribosomal protein S24

MacromoleculeName: Ribosomal protein S24 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 14.872646 KDa
SequenceString:
MPEITVKVRK VLNNPLLQRQ QCVVDVLHPG CTYESKEAIK AKVAQQLKVA DQKNIVLYGF KTSFGGGHTV GFCNAYQNMD ALMKYEPGF RKIRCGLIEA PKPVSRKQLK NLKNRRLKKR GTEKATVTLG AKK

UniProtKB: Ribosomal protein S24

+
Macromolecule #26: 40S ribosomal protein S25

MacromoleculeName: 40S ribosomal protein S25 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 10.121098 KDa
SequenceString:
MSSKKWTKKA VKEKVDYPTL FADEAAMNEA LKFIKNSKCI THTQICERLR VSVALAKRVM RQLVKSGDFA IVSKSSRMTI FKNMTKKE

UniProtKB: 40S ribosomal protein S25

+
Macromolecule #27: 40S ribosomal protein S26

MacromoleculeName: 40S ribosomal protein S26 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 12.791023 KDa
SequenceString:
MPVKRRNNGR SKYNCGHTNI VRCQNCHRCV PKDKVIKRFT IRNIVDNTIA DDVLNACVIQ GFAIPKLYNK VQYCVSCSIH NHIVRVRSR EDRKIRTPPK RFPRNSSQKK

UniProtKB: 40S ribosomal protein S26

+
Macromolecule #28: Ribosomal protein S27

MacromoleculeName: Ribosomal protein S27 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 14.117312 KDa
SequenceString:
MTPFSRFGEH CQLNINHAVY TLKLQTNPNK FKFKSELRGA KVSMNVDLLY PDPVEEQRKH KLKRLVQGPN SYFLEIKCAG CQDIVVVYS HANTPVFCPG CTSQISIPTG GKCAFTSQVE RYRQK

UniProtKB: Ribosomal protein S27

+
Macromolecule #29: Ribosomal protein S28

MacromoleculeName: Ribosomal protein S28 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 7.358642 KDa
SequenceString:
MPEPINARVI EVLGRTSSRG GITQVKVEFM TGEKRQIIRN VIGPVRKDDI LVLMESEREA RRLR

UniProtKB: Ribosomal protein S28

+
Macromolecule #30: Ribosomal protein S29A

MacromoleculeName: Ribosomal protein S29A / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 15.49978 KDa
SequenceString:
MRSALDTGVA ADRIGRPQTF AELRVDKVDD IGTQRHIEHL GPRKLRNLGS CGAEDLDSRV HPSTIFWPTE ADNINLASGV PKKGPSMRE TEFCTHIAHK RECRICGNYN SVYRKYGLFI CRRCFKENAG KIGFVKLH

UniProtKB: Ribosomal protein S29A

+
Macromolecule #31: Ribosomal protein S27a

MacromoleculeName: Ribosomal protein S27a / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 15.134745 KDa
SequenceString:
MLVIVRLQDQ TLPFELPAGA RASQLSNLLS SSGMAFSLHT QGRVLSEAAE LNDKMVIDAF VPADGAGKDK KRKKKAHKTP KKIKHEPKK VRLACLKYYT IKGDTAEPTR EYCPNCGPGI RIARHADRCH CGRCGFAK

UniProtKB: Ribosomal protein S27a

+
Macromolecule #33: Ribosomal protein S12

MacromoleculeName: Ribosomal protein S12 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 14.378715 KDa
SequenceString:
MADTTRENFL KETFKRIHNM DGLVTGHRQV FKYLERKRAK ICFLASDCEE KQYADIVECL CKEYKVHLCK KFTRRTLGEL TGQVRCLAD SDKIIKVVPA SACVIHNFVG MSSGDVDSFL TKLDEQ

UniProtKB: Ribosomal protein S12

+
Macromolecule #34: 40S ribosomal protein S30

MacromoleculeName: 40S ribosomal protein S30 / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Molecular weightTheoretical: 7.932407 KDa
SequenceString:
MARAHGGLTS AGKVRKCTPK KEKKEKPRPP RGRAYKRLLY NKNFVDDTLI HNGRRLGPNN LLIRQKLGF

UniProtKB: 40S ribosomal protein S30

+
Macromolecule #35: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 35 / Number of copies: 23 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #36: emetine

MacromoleculeName: emetine / type: ligand / ID: 36 / Number of copies: 1 / Formula: YAT
Molecular weightTheoretical: 480.639 Da
Chemical component information

ChemComp-34G:
emetine / Emetine

+
Macromolecule #37: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 37 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #38: water

MacromoleculeName: water / type: ligand / ID: 38 / Number of copies: 743 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 72.26 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xy3

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 289618
FSC plot (resolution estimation)

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