[English] 日本語
Yorodumi
- PDB-8bsi: Giardia ribosome chimeric hybrid-like GDP+Pi bound state (B1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bsi
TitleGiardia ribosome chimeric hybrid-like GDP+Pi bound state (B1)
Components
  • (40S ribosomal protein ...) x 10
  • (60S ribosomal protein ...) x 6
  • (Ribosomal protein ...) x 52
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • E-site tRNA
  • Elongation factor 2EEF2
  • Large Subunit rRNA
  • Ribosomal L22e
  • Ribosomal L38e
  • Small Subunit rRNA
  • Ubiquitin/Ribosomal protein L40e
  • mRNAMessenger RNA
KeywordsRIBOSOME / Translation / Giardia / Eukaryote / Eukaryotic / Macromolecule / tRNA / EF-2 / Elongation / GDP
Function / homology
Function and homology information


translational elongation / 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) / translation elongation factor activity / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / small-subunit processome ...translational elongation / 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) / translation elongation factor activity / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / small-subunit processome / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / protein tag activity / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / small ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / nucleolus / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Ribosomal protein L40e, archaeal / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Ribosomal protein L41 / Ribosomal protein L41 / Elongation factor EFG, domain V-like ...Ribosomal protein L40e, archaeal / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Ribosomal protein L41 / Ribosomal protein L41 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / metallochaperone-like domain / TRASH domain / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein L29e / Ribosomal protein S26e / Ribosomal protein S25 / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L29e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S30 / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein L24e, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S4e, N-terminal, conserved site / 40S ribosomal protein S4, C-terminal domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal S17 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal protein L23/L25, N-terminal / Ribosomal L38e protein family / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L22e protein family / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1 / 40S Ribosomal protein S10 / 60S ribosomal protein L35 / Ribosomal protein S27 / Ribosomal protein L35Ae, conserved site / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S3Ae / Plectin/S10, N-terminal / Ribosomal S3Ae family / Ribosomal protein S7e / Ribosomal L27e protein family / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L31e, conserved site / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L34e
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L39 / Ribosomal protein S27 ...GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L39 / Ribosomal protein S27 / 40S ribosomal protein S30 / Ribosomal protein S19e / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS2 / Ribosomal protein L10a / Ribosomal protein L29 / Large ribosomal subunit protein eL22 / Ribosomal protein L27 / 40S ribosomal protein S8 / Ribosomal protein L21 / Ribosomal L38e / 40S ribosomal protein S21 / Ribosomal protein S28 / Ribosomal protein L14 / Ribosomal protein S20 / Ribosomal protein L18 / Ribosomal protein S24 / Ribosomal protein L30 / 40S ribosomal protein S6 / 60S ribosomal protein L13 / Ribosomal protein S29A / Ribosomal protein L4 / Ribosomal protein L24 / 40S ribosomal protein S25 / 40S ribosomal protein S3 / Ribosomal protein L15 / Ribosomal protein S15 / Ribosomal protein S13 / Ribosomal protein L17 / 40S ribosomal protein S4 / Ribosomal protein L26 / Ribosomal protein L19 / Ribosomal protein L11 / Ribosomal protein S16 / Ribosomal protein L35a / Ribosomal protein S9 / 60S ribosomal protein L7a / Ribosomal protein L37 / Ribosomal protein L10 / Ribosomal protein L32 / Large ribosomal subunit protein eL34 / Ribosomal protein L31B / Ribosomal protein L23A / Ribosomal protein S2 / Ribosomal protein L37a / Ribosomal protein L6 / Ribosomal protein L44 / 40S ribosomal protein S26 / Ribosomal protein S17 / Ribosomal protein S10B / Ribosomal protein L7 / Ribosomal protein L3 / Ribosomal protein L23 / Ribosomal protein S23 / 60S ribosomal protein L18a / 40S ribosomal protein S7 / Elongation factor 2 / Ribosomal protein L13a / Ribosomal protein S11 / 50S ribosomal protein L40e / Ribosomal protein L36-1 / 60S ribosomal protein L29 / Ribosomal protein S18 / Ribosomal protein L27a / Ribosomal protein S5 / Ribosomal protein L2 / Ribosomal protein L5 / Ribosomal protein S15A / Ribosomal protein S14 / 60S ribosomal protein L41
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMajumdar, S. / Emmerich, A.G. / Sanyal, S.
Funding support Sweden, United States, 7items
OrganizationGrant numberCountry
Swedish Research Council2016-06264 Sweden
Swedish Research Council2018-05946 Sweden
Swedish Research Council2018-05498 Sweden
Knut and Alice Wallenberg FoundationKAW 2017.0055 Sweden
Carl Trygger FoundationCTS 18:338 Sweden
Carl Trygger FoundationCTS 19:806 Sweden
Wenner-Gren FoundationUPD2017:0238 United States
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis.
Authors: Soneya Majumdar / Andrew Emmerich / Sascha Krakovka / Chandra Sekhar Mandava / Staffan G Svärd / Suparna Sanyal /
Abstract: Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated ...Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated translocation intermediates, from ribosomes isolated directly from actively growing Giardia cells. The highly compact and uniquely GC-rich Giardia ribosomes possess eukaryotic rRNAs and ribosomal proteins, but retain some bacterial features. The translocation intermediates, with naturally bound tRNAs and eukaryotic elongation factor 2 (eEF2), display characteristic ribosomal intersubunit rotation and small subunit's head swiveling-universal for translocation. In addition, we observe the eukaryote-specific 'subunit rolling' dynamics, albeit with limited features. Finally, the eEF2·GDP state features a uniquely positioned 'leaving phosphate (Pi)' that proposes hitherto unknown molecular events of Pi and eEF2 release from the ribosome at the final stage of translocation. In summary, our study elucidates the mechanism of translocation in the protists and illustrates evolution of the translation machinery from bacteria to eukaryotes from both the structural and mechanistic perspectives.
History
DepositionNov 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
LA: Ribosomal protein L2
LB: Ribosomal protein L3
LC: Ribosomal protein L4
LD: 5.8S rRNA
LE: 5S rRNA
LF: Ribosomal protein L5
LG: Ribosomal protein L39
LH: Ribosomal protein L7
LI: 60S ribosomal protein L7a
LJ: Ribosomal protein L6
LK: Ribosomal protein L10
LL: Ribosomal protein L11
LM: 60S ribosomal protein L13
LN: Ribosomal protein L14
LO: Ribosomal protein L15
LP: Ribosomal protein L13a
LQ: Ribosomal protein L17
LR: Ribosomal protein L18
LS: Ribosomal protein L19
LT: 60S ribosomal protein L18a
LU: Ribosomal protein L21
LV: Ribosomal L22e
LW: Ribosomal protein L23
LX: Ribosomal protein L24
LY: Ribosomal protein L23A
LZ: Ribosomal protein L26
La: 60S ribosomal protein L27
Lb: Ribosomal protein L27a
Lc: 60S ribosomal protein L29
Ld: Ribosomal protein L30
Le: Ribosomal protein L31B
Lf: Ribosomal protein L32
Lg: Ribosomal protein L35a
Lh: Ribosomal protein L34
Li: Ribosomal protein L29
Lj: Ribosomal protein L36-1
Lk: Ribosomal protein L37
Ll: Ribosomal L38e
Ln: Ribosomal protein L10a
Lo: 60S ribosomal protein L41
Lp: Ribosomal protein L44
Lq: Ribosomal protein L37a
Ls: Ubiquitin/Ribosomal protein L40e
Lt: Large Subunit rRNA
Lu: E-site tRNA
SA: 40S ribosomal protein SA
SB: Ribosomal protein S2
SC: Ribosomal protein S3
SD: 40S ribosomal protein S3a
SE: 40S ribosomal protein S4
SF: Ribosomal protein S5
SG: 40S ribosomal protein S6
SH: 40S ribosomal protein S7
SI: 40S ribosomal protein S8
SJ: Ribosomal protein S15A
SK: Ribosomal protein S9
SL: Ribosomal protein S10B
SM: Ribosomal protein S11
SO: Ribosomal protein S23
SP: Ribosomal protein S13
SQ: Ribosomal protein S14
SR: Ribosomal protein S15
ST: Ribosomal protein S16
SU: Ribosomal protein S17
SV: Ribosomal protein S18
SW: Ribosomal protein S19e
SX: Ribosomal protein S20
SY: 40S ribosomal protein S21
Sb: Ribosomal protein S24
Sc: 40S ribosomal protein S25
Sd: 40S ribosomal protein S26
Se: Ribosomal protein S27
Sg: Ribosomal protein S28
Sh: Ribosomal protein S29A
Sj: 40S ribosomal protein S30
St: Small Subunit rRNA
a: Elongation factor 2
y: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,835,18480
Polymers2,834,64578
Non-polymers5382
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Ribosomal protein ... , 52 types, 52 molecules LALBLCLFLGLHLJLKLLLNLOLPLQLRLSLULWLXLYLZLbLdLeLfLgLhLiLjLkLn...

#1: Protein Ribosomal protein L2 /


Mass: 27090.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: E2RTN4
#2: Protein Ribosomal protein L3 /


Mass: 42715.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BRZ3
#3: Protein Ribosomal protein L4 / 60S ribosomal protein L4


Mass: 35048.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B7H8
#6: Protein Ribosomal protein L5 / 60S ribosomal protein L5


Mass: 33961.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: E2RU47
#7: Protein Ribosomal protein L39 /


Mass: 6353.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644EZB9
#8: Protein Ribosomal protein L7 /


Mass: 27103.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BRY6
#10: Protein Ribosomal protein L6 /


Mass: 20889.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BNT5
#11: Protein Ribosomal protein L10 /


Mass: 24283.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BM86
#12: Protein Ribosomal protein L11 /


Mass: 19767.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BI95
#14: Protein Ribosomal protein L14 /


Mass: 14785.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B4F8
#15: Protein Ribosomal protein L15 /


Mass: 24353.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B8Z6
#16: Protein Ribosomal protein L13a / Ribosome


Mass: 22921.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BU75
#17: Protein Ribosomal protein L17 /


Mass: 18722.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BE76
#18: Protein Ribosomal protein L18 /


Mass: 20207.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B4T7
#19: Protein Ribosomal protein L19 /


Mass: 23199.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BH61
#21: Protein Ribosomal protein L21 /


Mass: 18296.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B2Q4
#23: Protein Ribosomal protein L23 /


Mass: 15450.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BS37
#24: Protein Ribosomal protein L24 /


Mass: 22751.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B7P2
#25: Protein Ribosomal protein L23A / Ribosome


Mass: 16053.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BMP6
#26: Protein Ribosomal protein L26 /


Mass: 15621.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BFT3
#28: Protein Ribosomal protein L27a / Ribosome


Mass: 17166.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BZ78
#30: Protein Ribosomal protein L30 /


Mass: 11698.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B5N7
#31: Protein Ribosomal protein L31B / Ribosome


Mass: 12184.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BMP3
#32: Protein Ribosomal protein L32 /


Mass: 15985.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BMD9
#33: Protein Ribosomal protein L35a / Ribosome


Mass: 13913.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BKK5
#34: Protein Ribosomal protein L34 /


Mass: 13528.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BMF7
#35: Protein Ribosomal protein L29 /


Mass: 14292.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644FBK5
#36: Protein Ribosomal protein L36-1 / Ribosome


Mass: 10586.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BYA6
#37: Protein Ribosomal protein L37 /


Mass: 10329.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BLV7
#39: Protein Ribosomal protein L10a / Ribosome


Mass: 24630.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644FB74
#41: Protein Ribosomal protein L44 /


Mass: 12311.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BQU8
#42: Protein Ribosomal protein L37a / Ribosome


Mass: 10508.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BN26
#47: Protein Ribosomal protein S2 /


Mass: 26765.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BMZ1
#48: Protein Ribosomal protein S3 /


Mass: 24779.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B8Z2
#51: Protein Ribosomal protein S5 /


Mass: 21058.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BZD3
#55: Protein Ribosomal protein S15A / Ribosome


Mass: 14770.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: E2RU77
#56: Protein Ribosomal protein S9 /


Mass: 21699.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BKS8
#57: Protein Ribosomal protein S10B / Ribosome


Mass: 15406.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BRX3
#58: Protein Ribosomal protein S11 /


Mass: 18104.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BVU0
#59: Protein Ribosomal protein S23 /


Mass: 15897.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BS96
#60: Protein Ribosomal protein S13 /


Mass: 17627.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BE02
#61: Protein Ribosomal protein S14 /


Mass: 15755.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: E2RU83
#62: Protein Ribosomal protein S15 /


Mass: 16728.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BBP3
#63: Protein Ribosomal protein S16 /


Mass: 17634.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BKC6
#64: Protein Ribosomal protein S17 /


Mass: 15787.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BRG5
#65: Protein Ribosomal protein S18 /


Mass: 17510.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BZ58
#66: Protein Ribosomal protein S19e / Ribosome


Mass: 15463.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644F964
#67: Protein Ribosomal protein S20 /


Mass: 14073.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B4G0
#69: Protein Ribosomal protein S24 /


Mass: 14872.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B593
#72: Protein Ribosomal protein S27 /


Mass: 9144.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644F5K9
#73: Protein Ribosomal protein S28 /


Mass: 7358.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B4F3
#74: Protein Ribosomal protein S29A / Ribosome


Mass: 6142.263 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B7H6

-
RNA chain , 6 types, 6 molecules LDLELtLuSty

#4: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 45891.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: GenBank: 9954289
#5: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38993.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: GenBank: 2333213664
#44: RNA chain Large Subunit rRNA


Mass: 874762.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote)
#45: RNA chain E-site tRNA


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote)
#76: RNA chain Small Subunit rRNA


Mass: 471227.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote)
#78: RNA chain mRNA / Messenger RNA


Mass: 3562.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote)

-
60S ribosomal protein ... , 6 types, 6 molecules LILMLTLaLcLo

#9: Protein 60S ribosomal protein L7a /


Mass: 25427.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BLL7
#13: Protein 60S ribosomal protein L13 /


Mass: 26640.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B6M8
#20: Protein 60S ribosomal protein L18a /


Mass: 20624.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BT04
#27: Protein 60S ribosomal protein L27 /


Mass: 15374.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B1T3
#29: Protein 60S ribosomal protein L29 /


Mass: 7363.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BYY2
#40: Protein/peptide 60S ribosomal protein L41 /


Mass: 3283.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: V6TX21

-
Protein , 4 types, 4 molecules LVLlLsa

#22: Protein Ribosomal L22e


Mass: 14427.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644FC41
#38: Protein Ribosomal L38e


Mass: 8605.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B481
#43: Protein Ubiquitin/Ribosomal protein L40e


Mass: 14343.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BXE1
#77: Protein Elongation factor 2 / EEF2


Mass: 99759.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BU59

-
40S ribosomal protein ... , 10 types, 10 molecules SASDSESGSHSISYScSdSj

#46: Protein 40S ribosomal protein SA /


Mass: 28101.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644FB17
#49: Protein 40S ribosomal protein S3a /


Mass: 28413.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644F9A2
#50: Protein 40S ribosomal protein S4 /


Mass: 30464.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BFE3
#52: Protein 40S ribosomal protein S6 /


Mass: 28084.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B6L8
#53: Protein 40S ribosomal protein S7 /


Mass: 21786.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BT38
#54: Protein 40S ribosomal protein S8 /


Mass: 19451.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B252
#68: Protein 40S ribosomal protein S21 /


Mass: 9686.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B484
#70: Protein 40S ribosomal protein S25 /


Mass: 10121.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B8H7
#71: Protein 40S ribosomal protein S26 /


Mass: 12791.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BQZ7
#75: Protein 40S ribosomal protein S30 /


Mass: 7932.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644F843

-
Non-polymers , 2 types, 2 molecules

#79: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#80: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Giardia ribosome chimeric hybrid-like GDP+Pi bound state (B1)
Type: RIBOSOME / Entity ID: #1-#78 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Giardia intestinalis (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1900 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35694 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more