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- PDB-8b2l: Cryo-EM structure of the plant 80S ribosome -

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Basic information

Entry
Database: PDB / ID: 8b2l
TitleCryo-EM structure of the plant 80S ribosome
Components
  • (40S ribosomal protein ...) x 30
  • (60S ribosomal protein ...) x 22
  • (Ribosomal protein ...) x 3
  • 18S rRNA18S ribosomal RNA
  • 25S rRNA
  • 30S ribosomal protein S15, chloroplasticRibosome
  • 5.8S rRNA5.8S ribosomal RNA
  • 50S ribosomal protein L22, chloroplasticRibosome
  • 5S rRNA5S ribosomal RNA
  • eL27 (60S ribosomal protein L27)
  • eL28 (60S ribosomal protein L28)
  • eL31 (60S ribosomal protein L31)
  • eL33 (60S ribosomal protein L35a)
  • eL36 (60S ribosomal protein L36)
  • eL6 (60S ribosomal protein L6)
  • guanine nucleotide-binding protein subunit beta-like protein
  • mRNAMessenger RNA
  • nascent chain
  • tRNATransfer RNA
  • uL13 (60S ribosomal protein L13a)
  • uL15 (60S ribosomal protein L27a)
  • uL16 (60S ribosomal protein L10)
  • uL2 (60S ribosomal protein L8)
  • uL24 (60S ribosomal protein L26)
  • uL3 (60S ribosomal protein L3)
  • uL4 (60S ribosomal protein L4)
  • uL5 (60S ribosomal protein L11)
  • uL6 (60S ribosomal protein L9)
  • ubiquitin-40S ribosomal protein S27a-like
  • ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / Plant / 80S / rRNA Modifications
Function / homology
Function and homology information


endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / protein-RNA complex assembly / 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) / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / protein-RNA complex assembly / 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) / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA / small-subunit processome / protein kinase C binding / modification-dependent protein catabolic process / rRNA processing / ribosomal small subunit biogenesis / protein tag activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / ribosome binding / ribosome biogenesis / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein L41 / Ribosomal protein L41 / : ...Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / metallochaperone-like domain / TRASH domain / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / Ribosomal protein L29e / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein S26e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S25 / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal L29e protein family / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L10e / S25 ribosomal protein / Ribosomal protein S21e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S30 / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8e, conserved site / Ribosomal protein L24e, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein L34e, conserved site / 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 S19e signature. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal S17 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal protein L23/L25, N-terminal / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L22e protein family / Ribosomal protein S17, archaeal/eukaryotic / 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 L30e, 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 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 L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family
Similarity search - Domain/homology
: / SPERMIDINE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / SPERMIDINE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S25 / 60S ribosomal protein L35-like / 60S ribosomal protein L30-like / Ubiquitin-60S ribosomal protein L40 / Ribosomal protein L19 / 60S ribosomal protein L4-like / 60S ribosomal protein L37a / 40S ribosomal protein S14-2 / 60S ribosomal protein L11-1 / 40S ribosomal protein S2-3-like / 60S ribosomal protein L21-1-like / 60S ribosomal protein L5-like / 40S ribosomal protein S30 / 40S ribosomal protein S20-2 / 40S ribosomal protein S27 / 60S ribosomal protein L23 / 60S ribosomal protein L35a-3 / 60S ribosomal protein L8-like / 60S ribosomal protein L31 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S19-3 / 40S ribosomal protein S18 / 60S ribosomal protein L29 / 60S ribosomal protein L39-3 / 60S ribosomal protein L10-like / 60S ribosomal protein L32-1 / 40S ribosomal protein S6 / 40S ribosomal protein S7 / 40S ribosomal protein S17-like / 60S ribosomal protein L3 / 40S ribosomal protein S13 / 40S ribosomal protein S24 / 40S ribosomal protein S21 / 60S ribosomal protein L7-4-like / 60S ribosomal protein L14-1 / Guanine nucleotide-binding protein subunit beta-like protein / 60S ribosomal protein L27 / 40S ribosomal protein S28 / 40S ribosomal protein S16 / 60S ribosomal protein L44 / 60S ribosomal protein L6-like isoform X1 / 40S ribosomal protein S12 / 40S ribosomal protein S9-2-like / 60S ribosomal protein L27a-3-like / 60S ribosomal protein L24-like / 60S ribosomal protein L22-2-like / 40S ribosomal protein S11-like / 40S ribosomal protein S5-like / 40S ribosomal protein S3-2-like / 60S ribosomal protein L9-1-like / Ubiquitin-40S ribosomal protein S27a-like / 60S ribosomal protein L38 / 40S ribosomal protein S23 / 60S ribosomal protein L17-1-like / 60S ribosomal protein L18a / 60S ribosomal protein L13 / 40S ribosomal protein S26 / 40S ribosomal protein S8 / 60S ribosomal protein L28-1-like / 60S ribosomal protein L36 / Ribosomal protein L15 / 60S ribosomal protein L7a / 40S ribosomal protein S15a-1 / 60S ribosomal protein L18-2-like / 40S ribosomal protein S15-like / 40S ribosomal protein S10-1-like / 60S ribosomal protein L13a-4 / Ribosomal protein L37 / 60S ribosomal protein L26-1-like / 40S ribosomal protein S29 / 40S ribosomal protein S4 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS1
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsSmirnova, J. / Loerke, J. / Kleinau, G. / Schmidt, A. / Buerger, J. / Meyer, E.H. / Mielke, T. / Scheerer, P. / Bock, R. / Spahn, C.M.T. / Zoschke, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)416210002 Germany
CitationJournal: Nat Plants / Year: 2023
Title: Structure of the actively translating plant 80S ribosome at 2.2 Å resolution.
Authors: Julia Smirnova / Justus Loerke / Gunnar Kleinau / Andrea Schmidt / Jörg Bürger / Etienne H Meyer / Thorsten Mielke / Patrick Scheerer / Ralph Bock / Christian M T Spahn / Reimo Zoschke /
Abstract: In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are ...In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing.
History
DepositionSep 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: 40S ribosomal protein S4
k1: 40S ribosomal protein S6
h1: 18S rRNA
l1: 40S ribosomal protein S10-1-like
C1: 40S ribosomal protein S12
D1: 40S ribosomal protein S17-like
E1: 40S ribosomal protein S19-3
F1: 40S ribosomal protein S3a
G1: 40S ribosomal protein S21
H1: 40S ribosomal protein S24
I1: 40S ribosomal protein S25
J1: 40S ribosomal protein S26
K1: 40S ribosomal protein S27
L1: 40S ribosomal protein S28
M1: 40S ribosomal protein S30
N1: ubiquitin-40S ribosomal protein S27a-like
O1: 40S ribosomal protein S7
P1: 40S ribosomal protein S8
Q1: guanine nucleotide-binding protein subunit beta-like protein
R1: 40S ribosomal protein S20-2
S1: 40S ribosomal protein S14-2
T1: 40S ribosomal protein S23
U1: 40S ribosomal protein S18
V1: 40S ribosomal protein S29
W1: 30S ribosomal protein S15, chloroplastic
X1: 40S ribosomal protein S11-like
Y1: 40S ribosomal protein S15-like
Z1: 40S ribosomal protein SA
a1: 40S ribosomal protein S3-2-like
b1: 40S ribosomal protein S9-2-like
c1: 40S ribosomal protein S2-3-like
d1: 40S ribosomal protein S5-like
e1: 40S ribosomal protein S15a-1
f1: 40S ribosomal protein S16
B1: mRNA
i2: tRNA
W2: tRNA
C3: 5S rRNA
D3: 60S ribosomal protein L13
E3: 60S ribosomal protein L14-1
F3: Ribosomal protein L15
G3: 60S ribosomal protein L18-2-like
H3: Ribosomal protein L19
I3: 60S ribosomal protein L18a
J3: 60S ribosomal protein L21-1-like
K3: 60S ribosomal protein L22-2-like
L3: 60S ribosomal protein L24-like
M3: eL27 (60S ribosomal protein L27)
N3: eL28 (60S ribosomal protein L28)
O3: 60S ribosomal protein L29
P3: 60S ribosomal protein L30-like
Q3: eL31 (60S ribosomal protein L31)
R3: 60S ribosomal protein L32-1
S3: eL33 (60S ribosomal protein L35a)
T3: 60S ribosomal protein L34
U3: eL36 (60S ribosomal protein L36)
V3: Ribosomal protein L37
W3: 60S ribosomal protein L38
X3: 60S ribosomal protein L39-3
Y3: ubiquitin-60S ribosomal protein L40
p3: 60S ribosomal protein L41
Z3: 60S ribosomal protein L44
a3: 60S ribosomal protein L37a
b3: eL6 (60S ribosomal protein L6)
c3: 60S ribosomal protein L7a
d3: uL13 (60S ribosomal protein L13a)
e3: 60S ribosomal protein L23
f3: uL15 (60S ribosomal protein L27a)
g3: uL16 (60S ribosomal protein L10)
h3: 60S ribosomal protein L5-like
j3: 50S ribosomal protein L22, chloroplastic
k3: 60S ribosomal protein L23a
m3: uL24 (60S ribosomal protein L26)
n3: 60S ribosomal protein L35-like
o3: uL2 (60S ribosomal protein L8)
q3: 60S ribosomal protein L7-4-like
r3: uL3 (60S ribosomal protein L3)
s3: uL4 (60S ribosomal protein L4)
t3: uL5 (60S ribosomal protein L11)
u3: uL6 (60S ribosomal protein L9)
l3: nascent chain
A3: 25S rRNA
B3: 5.8S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,262,705373
Polymers3,252,15183
Non-polymers10,554290
Water122,3586792
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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40S ribosomal protein ... , 30 types, 30 molecules A1k1l1C1D1E1F1G1H1I1J1K1L1M1O1P1R1S1T1U1V1X1Y1Z1a1b1c1d1e1f1

#1: Protein 40S ribosomal protein S4 /


Mass: 29971.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DQ51
#2: Protein 40S ribosomal protein S6 /


Mass: 28368.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Z3Y7
#4: Protein 40S ribosomal protein S10-1-like / Ribosome


Mass: 23121.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DHU6
#5: Protein 40S ribosomal protein S12 /


Mass: 15190.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4B129
#6: Protein 40S ribosomal protein S17-like /


Mass: 16643.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Z9G2
#7: Protein 40S ribosomal protein S19-3 / Ribosome


Mass: 16034.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Y949
#8: Protein 40S ribosomal protein S3a / / Protein cyc07


Mass: 29782.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: Q285L8
#9: Protein 40S ribosomal protein S21 /


Mass: 9307.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4A3T4
#10: Protein 40S ribosomal protein S24 /


Mass: 15429.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3ZXI6
#11: Protein 40S ribosomal protein S25 /


Mass: 11795.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A076L2E2
#12: Protein 40S ribosomal protein S26 /


Mass: 14540.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CWI7
#13: Protein 40S ribosomal protein S27 /


Mass: 9613.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XJK0
#14: Protein 40S ribosomal protein S28 /


Mass: 7481.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4AS05
#15: Protein 40S ribosomal protein S30 /


Mass: 6953.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XGJ0
#17: Protein 40S ribosomal protein S7 /


Mass: 22121.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Z906
#18: Protein 40S ribosomal protein S8 /


Mass: 25164.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CZK3
#20: Protein 40S ribosomal protein S20-2 / Ribosome


Mass: 13651.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XHL0
#21: Protein 40S ribosomal protein S14-2 / Ribosome


Mass: 16375.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XAN1
#22: Protein 40S ribosomal protein S23 /


Mass: 15771.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4C879
#23: Protein 40S ribosomal protein S18 /


Mass: 17578.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3YM01
#24: Protein 40S ribosomal protein S29 /


Mass: 6455.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DPT4
#26: Protein 40S ribosomal protein S11-like /


Mass: 17724.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BW10
#27: Protein 40S ribosomal protein S15-like /


Mass: 17274.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DFI4
#28: Protein 40S ribosomal protein SA /


Mass: 35894.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Y4M0
#29: Protein 40S ribosomal protein S3-2-like / Ribosome


Mass: 27758.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BXU2
#30: Protein 40S ribosomal protein S9-2-like / Ribosome


Mass: 23103.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4B907
#31: Protein 40S ribosomal protein S2-3-like / Ribosome


Mass: 30652.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XAX8
#32: Protein 40S ribosomal protein S5-like /


Mass: 23373.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BXT5
#33: Protein 40S ribosomal protein S15a-1 / Ribosome / 40S ribosomal protein S15a-1 isoform X1


Mass: 14815.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DBQ8
#34: Protein 40S ribosomal protein S16 /


Mass: 16731.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4AU23

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RNA chain , 6 types, 7 molecules h1B1i2W2C3A3B3

#3: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 583622.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco)
#35: RNA chain mRNA / Messenger RNA


Mass: 3629.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco)
#36: RNA chain tRNA / Transfer RNA


Mass: 24571.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: GenBank: 19120
#37: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38328.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: GenBank: 2276356346
#81: RNA chain 25S rRNA


Mass: 1098268.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco)
#82: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 52563.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: GenBank: 1782605526

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Protein , 20 types, 20 molecules N1Q1W1M3N3Q3S3U3Y3b3d3f3g3j3m3o3r3s3t3u3

#16: Protein ubiquitin-40S ribosomal protein S27a-like


Mass: 17739.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4C0C1
#19: Protein guanine nucleotide-binding protein subunit beta-like protein


Mass: 36061.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4ABX7
#25: Protein 30S ribosomal protein S15, chloroplastic / Ribosome


Mass: 17099.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3ZRI7
#47: Protein eL27 (60S ribosomal protein L27)


Mass: 15722.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4AEL0
#48: Protein eL28 (60S ribosomal protein L28)


Mass: 15954.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4D1U6
#51: Protein eL31 (60S ribosomal protein L31)


Mass: 13894.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Y3V5
#53: Protein eL33 (60S ribosomal protein L35a)


Mass: 12959.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XU79
#55: Protein eL36 (60S ribosomal protein L36)


Mass: 12361.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4D2I2
#59: Protein ubiquitin-60S ribosomal protein L40


Mass: 14717.386 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3X011
#63: Protein eL6 (60S ribosomal protein L6)


Mass: 25536.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4B0G2
#65: Protein uL13 (60S ribosomal protein L13a)


Mass: 23525.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DN49
#67: Protein uL15 (60S ribosomal protein L27a)


Mass: 16578.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BFD5
#68: Protein uL16 (60S ribosomal protein L10)


Mass: 25012.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Z2D7
#70: Protein 50S ribosomal protein L22, chloroplastic / Ribosome


Mass: 20136.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CCH0
#72: Protein uL24 (60S ribosomal protein L26)


Mass: 16748.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DPM5
#74: Protein uL2 (60S ribosomal protein L8)


Mass: 28220.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XXQ5
#76: Protein uL3 (60S ribosomal protein L3)


Mass: 44507.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3ZLI9
#77: Protein uL4 (60S ribosomal protein L4)


Mass: 44706.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3X0M5
#78: Protein uL5 (60S ribosomal protein L11)


Mass: 20794.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XAW1
#79: Protein uL6 (60S ribosomal protein L9)


Mass: 22057.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4C068

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60S ribosomal protein ... , 22 types, 22 molecules D3E3G3I3J3K3L3O3P3R3T3W3X3p3Z3a3c3e3h3k3n3q3

#38: Protein 60S ribosomal protein L13 /


Mass: 23595.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CSN1
#39: Protein 60S ribosomal protein L14-1 / Ribosome


Mass: 15443.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4A807
#41: Protein 60S ribosomal protein L18-2-like / Ribosome


Mass: 20905.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DF55
#43: Protein 60S ribosomal protein L18a /


Mass: 21513.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CP52
#44: Protein 60S ribosomal protein L21-1-like / Ribosome


Mass: 18716.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XCW6
#45: Protein 60S ribosomal protein L22-2-like / Ribosome


Mass: 14277.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BSU3
#46: Protein 60S ribosomal protein L24-like /


Mass: 18606.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BHF2
#49: Protein 60S ribosomal protein L29 /


Mass: 7132.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3YR12
#50: Protein 60S ribosomal protein L30-like /


Mass: 12420.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3WZ09
#52: Protein 60S ribosomal protein L32-1 / Ribosome


Mass: 15665.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Z2X4
#54: Protein 60S ribosomal protein L34 /


Mass: 13788.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: P41098
#57: Protein 60S ribosomal protein L38 /


Mass: 8101.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4C4G8
#58: Protein 60S ribosomal protein L39-3 / Ribosome


Mass: 6503.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3YR32
#60: Protein/peptide 60S ribosomal protein L41 /


Mass: 3445.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: P62121
#61: Protein 60S ribosomal protein L44 /


Mass: 12037.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4AVP7
#62: Protein 60S ribosomal protein L37a /


Mass: 10280.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3X5Y9
#64: Protein 60S ribosomal protein L7a /


Mass: 29432.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4D668
#66: Protein 60S ribosomal protein L23 /


Mass: 15040.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XSQ1
#69: Protein 60S ribosomal protein L5-like /


Mass: 34627.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XE16
#71: Protein 60S ribosomal protein L23a / / L25


Mass: 17321.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: Q07761
#73: Protein 60S ribosomal protein L35-like /


Mass: 14352.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3WY31
#75: Protein 60S ribosomal protein L7-4-like / Ribosome


Mass: 28148.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4A5Z2

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Ribosomal protein ... , 3 types, 3 molecules F3H3V3

#40: Protein Ribosomal protein L15 /


Mass: 24228.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4D5P7
#42: Protein Ribosomal protein L19 /


Mass: 25055.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3X0I4
#56: Protein Ribosomal protein L37 /


Mass: 10879.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DN51

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Protein/peptide , 1 types, 1 molecules l3

#80: Protein/peptide nascent chain


Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco)

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Non-polymers , 6 types, 7082 molecules

#83: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 135 / Source method: obtained synthetically / Formula: Mg
#84: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 141 / Source method: obtained synthetically / Formula: K
#85: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#86: Chemical
ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H26N4
#87: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#88: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6792 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

-
Experiment

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

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Sample preparation

ComponentName: 40S subunit of the cytosolic 80S ribosome from tobacco
Type: RIBOSOME / Entity ID: #1-#82 / Source: NATURAL
Source (natural)Organism: Nicotiana tabacum (common tobacco)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 27 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335291 / Symmetry type: POINT

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