› 8auv

Electron Microscopy
2.38Å resolution

Cryo-EM structure of the plant 40S subunit

Released:
DOI: 10.2210/pdb8auv/pdb
PDB entry 8auv coloured by chain, front view.
PDB entry 8auv coloured by chain, side view.
PDB entry 8auv coloured by chain, top view.
Source organism: Nicotiana tabacum
Primary publication:
Structure of the actively translating plant 80S ribosome at 2.2 Å resolution.
Smirnova J, Loerke J, Kleinau G, Schmidt A, Bürger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R
OpenAccess logo Nat Plants (2023)
PMID: 37156858
Related structures: EMD-15674

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero 35-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-217142 (preferred)
Entry contents:
33 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (35 distinct):
40S ribosomal protein S4 Chain: A
Molecule details ›
Chain: A
Length: 264 amino acids
Theoretical weight: 29.97 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4DQ51 (Residues: 1-264; Coverage: 100%)
Gene name: LOC107832245
Sequence domains:
40S ribosomal protein S6 Chain: k
Molecule details ›
Chain: k
Length: 249 amino acids
Theoretical weight: 28.37 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3Z3Y7 (Residues: 1-249; Coverage: 100%)
Gene name: LOC107782679
Sequence domains: Ribosomal protein S6e
Plectin/eS10 N-terminal domain-containing protein Chain: l
Molecule details ›
Chain: l
Length: 208 amino acids
Theoretical weight: 23.12 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4DHU6 (Residues: 1-208; Coverage: 100%)
Gene name: LOC107829891
Sequence domains: Plectin/S10 domain
40S ribosomal protein S12 Chain: C
Molecule details ›
Chain: C
Length: 144 amino acids
Theoretical weight: 15.19 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4B129 (Residues: 1-144; Coverage: 100%)
Gene name: LOC107803315
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
40S ribosomal protein S17-like Chain: D
Molecule details ›
Chain: D
Length: 149 amino acids
Theoretical weight: 16.64 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3Z9G2 (Residues: 1-149; Coverage: 100%)
Gene name: LOC107784437
Sequence domains: Ribosomal S17
40S ribosomal protein S19-3 Chain: E
Molecule details ›
Chain: E
Length: 143 amino acids
Theoretical weight: 16.03 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3Y949 (Residues: 1-143; Coverage: 100%)
Gene name: LOC107773605
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein eS1 Chain: F
Molecule details ›
Chain: F
Length: 261 amino acids
Theoretical weight: 29.78 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: Q285L8 (Residues: 1-261; Coverage: 100%)
Gene name: cyc07
Sequence domains: Ribosomal S3Ae family
40S ribosomal protein S21 Chain: G
Molecule details ›
Chain: G
Length: 83 amino acids
Theoretical weight: 9.31 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4A3T4 (Residues: 1-83; Coverage: 100%)
Gene names: LOC107793454, LOC107800934
Sequence domains: Ribosomal protein S21e
40S ribosomal protein S24 Chain: H
Molecule details ›
Chain: H
Length: 133 amino acids
Theoretical weight: 15.43 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3ZXI6 (Residues: 1-133; Coverage: 100%)
Gene names: LOC107768485, LOC107775219, LOC107776707, LOC107791538
Sequence domains: Ribosomal protein S24e
40S ribosomal protein S25 Chain: I
Molecule details ›
Chain: I
Length: 107 amino acids
Theoretical weight: 11.8 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A076L2E2 (Residues: 1-107; Coverage: 100%)
Gene names: LOC107768022, LOC107807859, LOC107815372
Sequence domains: S25 ribosomal protein
40S ribosomal protein S26 Chain: J
Molecule details ›
Chain: J
Length: 127 amino acids
Theoretical weight: 14.54 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4CWI7 (Residues: 1-127; Coverage: 100%)
Gene names: LOC107782148, LOC107823272
Sequence domains: Ribosomal protein S26e
40S ribosomal protein S27 Chain: K
Molecule details ›
Chain: K
Length: 86 amino acids
Theoretical weight: 9.61 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3XJK0 (Residues: 1-86; Coverage: 100%)
Gene names: LOC107765692, LOC107808179
Sequence domains: Ribosomal protein S27
40S ribosomal protein S28 Chain: L
Molecule details ›
Chain: L
Length: 65 amino acids
Theoretical weight: 7.48 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4AS05 (Residues: 1-65; Coverage: 100%)
Gene names: LOC107774518, LOC107800747, LOC107812923, LOC107814175, LOC107825181
Sequence domains: Ribosomal protein S28e
40S ribosomal protein S30 Chain: M
Molecule details ›
Chain: M
Length: 62 amino acids
Theoretical weight: 6.95 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3XGJ0 (Residues: 1-62; Coverage: 100%)
Gene names: LOC107764876, LOC107796333, LOC107801831, LOC107805852, LOC107825161
Sequence domains: Ribosomal protein S30
Ubiquitin-like domain-containing protein Chain: N
Molecule details ›
Chain: N
Length: 156 amino acids
Theoretical weight: 17.74 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4C0C1 (Residues: 1-156; Coverage: 100%)
Gene names: LOC107813709, LOC107821919
Sequence domains:
40S ribosomal protein S7 Chain: O
Molecule details ›
Chain: O
Length: 191 amino acids
Theoretical weight: 22.12 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3Z906 (Residues: 1-191; Coverage: 100%)
Gene name: LOC107784137
Sequence domains: Ribosomal protein S7e
40S ribosomal protein S8 Chain: P
Molecule details ›
Chain: P
Length: 224 amino acids
Theoretical weight: 25.16 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4CZK3 (Residues: 1-224; Coverage: 100%)
Gene name: LOC107824336
Sequence domains: Ribosomal protein S8e
Guanine nucleotide-binding protein subunit beta-like protein Chain: Q
Molecule details ›
Chain: Q
Length: 328 amino acids
Theoretical weight: 36.06 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4ABX7 (Residues: 1-328; Coverage: 100%)
Gene name: LOC107795918
Sequence domains: WD domain, G-beta repeat
Small ribosomal subunit protein uS10 domain-containing protein Chain: R
Molecule details ›
Chain: R
Length: 122 amino acids
Theoretical weight: 13.65 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3XHL0 (Residues: 1-122; Coverage: 100%)
Gene names: LOC107765328, LOC107784562
Sequence domains: Ribosomal protein S10p/S20e
40S ribosomal protein S14-2 Chain: S
Molecule details ›
Chain: S
Length: 150 amino acids
Theoretical weight: 16.38 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3XAN1 (Residues: 1-150; Coverage: 100%)
Gene names: LOC107763058, LOC107808558
Sequence domains: Ribosomal protein S11
40S ribosomal protein S23 Chain: T
Molecule details ›
Chain: T
Length: 142 amino acids
Theoretical weight: 15.77 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4C879 (Residues: 1-142; Coverage: 100%)
Gene names: LOC107812875, LOC107813833, LOC107816169, LOC107816928, LOC107831185
Sequence domains: Ribosomal protein S12/S23
40S ribosomal protein S18 Chain: U
Molecule details ›
Chain: U
Length: 152 amino acids
Theoretical weight: 17.58 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3YM01 (Residues: 1-152; Coverage: 100%)
Gene name: LOC107777446
Sequence domains: Ribosomal protein S13/S18
40S ribosomal protein S29 Chain: V
Molecule details ›
Chain: V
Length: 56 amino acids
Theoretical weight: 6.46 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4DPT4 (Residues: 1-56; Coverage: 100%)
Gene names: LOC107770060, LOC107794864, LOC107797865, LOC107832143
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 N-terminal domain-containing protein Chain: W
Molecule details ›
Chain: W
Length: 151 amino acids
Theoretical weight: 17.1 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3ZRI7 (Residues: 1-151; Coverage: 100%)
Gene names: LOC107789793, LOC107790766, LOC107797659, LOC107803492, LOC107808791, LOC107816852
Sequence domains:
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chain: X
Molecule details ›
Chain: X
Length: 159 amino acids
Theoretical weight: 17.72 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4BW10 (Residues: 1-159; Coverage: 100%)
Gene names: LOC107780590, LOC107812432
Sequence domains:
40S ribosomal protein S15-like Chain: Y
Molecule details ›
Chain: Y
Length: 152 amino acids
Theoretical weight: 17.27 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4DFI4 (Residues: 1-152; Coverage: 100%)
Gene names: LOC107800576, LOC107829071
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS2 Chain: Z
Molecule details ›
Chain: Z
Length: 336 amino acids
Theoretical weight: 35.89 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3Y4M0 (Residues: 1-336; Coverage: 100%)
Gene name: LOC107772137
Sequence domains: Ribosomal protein S2
KH type-2 domain-containing protein Chain: a
Molecule details ›
Chain: a
Length: 248 amino acids
Theoretical weight: 27.76 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4BXU2 (Residues: 1-248; Coverage: 100%)
Gene name: LOC107813032
Sequence domains:
40S ribosomal protein S9-2-like Chain: b
Molecule details ›
Chain: b
Length: 197 amino acids
Theoretical weight: 23.1 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4B907 (Residues: 1-197; Coverage: 100%)
Gene names: LOC107805765, LOC107832770
Sequence domains:
S5 DRBM domain-containing protein Chain: c
Molecule details ›
Chain: c
Length: 280 amino acids
Theoretical weight: 30.65 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3XAX8 (Residues: 1-280; Coverage: 100%)
Gene name: LOC107763157
Sequence domains:
Small ribosomal subunit protein uS7 domain-containing protein Chain: d
Molecule details ›
Chain: d
Length: 210 amino acids
Theoretical weight: 23.37 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4BXT5 (Residues: 1-210; Coverage: 100%)
Gene name: LOC107812924
Sequence domains: Ribosomal protein S7p/S5e
40S ribosomal protein S15a-1 Chain: e
Molecule details ›
Chain: e
Length: 130 amino acids
Theoretical weight: 14.82 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4DBQ8 (Residues: 1-130; Coverage: 100%)
Gene names: LOC107763113, LOC107765652, LOC107799417, LOC107801674, LOC107814631, LOC107828126
Sequence domains: Ribosomal protein S8
40S ribosomal protein S16 Chain: f
Molecule details ›
Chain: f
Length: 147 amino acids
Theoretical weight: 16.73 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4AU23 (Residues: 1-147; Coverage: 100%)
Gene names: LOC107782068, LOC107801293
Sequence domains: Ribosomal protein S9/S16
18S Ribosomal RNA Chain: h
Molecule details ›
Chain: h
Length: 1808 nucleotides
Theoretical weight: 583.62 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
Messenger RNA Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.63 KDa

Ligands and Environments

5 bound ligands:
Ligand MG 76 x MG
Ligand K 47 x K
Ligand SPD 1 x SPD
Ligand SPM 3 x SPM
Ligand ZN 3 x ZN
7 modified residues:
Ligand A2M 12 x A2M
Ligand OMC 6 x OMC
Ligand PSU 41 x PSU
Ligand OMU 10 x OMU
Ligand OMG 5 x OMG
Ligand 6MZ 1 x 6MZ
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 2.38Å
Relevant EMDB volumes: EMD-15674

Quick links

Citations

1 citations in other articles

High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit.
Kravchenko et al. (2023)

1 mention without citation

Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action.
Weinhäupl et al. (2022)