› 8azw

Electron Microscopy
2.14Å resolution

Cryo-EM structure of the plant 60S subunit

Released:
DOI: 10.2210/pdb8azw/pdb
PDB entry 8azw coloured by chain, front view.
PDB entry 8azw coloured by chain, side view.
PDB entry 8azw 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-15773

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 46-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218417 (preferred)
Entry contents:
43 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (46 distinct):
60S ribosomal protein L13 Chain: D
Molecule details ›
Chain: D
Length: 206 amino acids
Theoretical weight: 23.6 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4CSN1 (Residues: 1-206; Coverage: 100%)
Gene name: LOC107822051
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14 domain-containing protein Chain: E
Molecule details ›
Chain: E
Length: 134 amino acids
Theoretical weight: 15.44 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4A807 (Residues: 1-134; Coverage: 100%)
Gene name: LOC107794709
Sequence domains: Ribosomal protein L14
Ribosomal protein L15 Chain: F
Molecule details ›
Chain: F
Length: 204 amino acids
Theoretical weight: 24.23 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4D5P7 (Residues: 1-204; Coverage: 100%)
Gene name: LOC107826284
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: G
Molecule details ›
Chain: G
Length: 187 amino acids
Theoretical weight: 20.91 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4DF55 (Residues: 1-187; Coverage: 100%)
Gene names: LOC107759208, LOC107829149
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Ribosomal protein L19 Chain: H
Molecule details ›
Chain: H
Length: 214 amino acids
Theoretical weight: 25.06 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3X0I4 (Residues: 1-214; Coverage: 100%)
Gene name: LOC107759916
Sequence domains: Ribosomal protein L19e
60S ribosomal protein L18a Chain: I
Molecule details ›
Chain: I
Length: 178 amino acids
Theoretical weight: 21.51 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4CP52 (Residues: 1-178; Coverage: 100%)
Gene names: LOC107775758, LOC107818966, LOC107820975, LOC107821623
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
60S ribosomal protein L21-1-like Chain: J
Molecule details ›
Chain: J
Length: 164 amino acids
Theoretical weight: 18.72 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3XCW6 (Residues: 1-164; Coverage: 100%)
Gene name: LOC107763612
Sequence domains: Ribosomal protein L21e
60S ribosomal protein L22-2-like Chain: K
Molecule details ›
Chain: K
Length: 127 amino acids
Theoretical weight: 14.28 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4BSU3 (Residues: 1-127; Coverage: 100%)
Gene name: LOC107811461
Sequence domains: Ribosomal L22e protein family
TRASH domain-containing protein Chain: L
Molecule details ›
Chain: L
Length: 164 amino acids
Theoretical weight: 18.61 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4BHF2 (Residues: 1-164; Coverage: 100%)
Gene names: LOC107781546, LOC107808292
Sequence domains: Ribosomal protein L24e
60S ribosomal protein L27 Chain: M
Molecule details ›
Chain: M
Length: 135 amino acids
Theoretical weight: 15.72 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4AEL0 (Residues: 1-135; Coverage: 100%)
Gene name: LOC107796761
Sequence domains:
Ribosomal eL28/Mak16 domain-containing protein Chain: N
Molecule details ›
Chain: N
Length: 143 amino acids
Theoretical weight: 15.95 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4D1U6 (Residues: 1-143; Coverage: 100%)
Gene name: LOC107824985
Sequence domains: Ribosomal L28e protein family
60S ribosomal protein L29 Chain: O
Molecule details ›
Chain: O
Length: 61 amino acids
Theoretical weight: 7.13 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3YR12 (Residues: 1-61; Coverage: 100%)
Gene name: LOC107778781
Sequence domains: Ribosomal L29e protein family
Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein Chain: P
Molecule details ›
Chain: P
Length: 113 amino acids
Theoretical weight: 12.42 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3WZ09 (Residues: 1-113; Coverage: 100%)
Gene names: LOC107759448, LOC107771134
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
60S ribosomal protein L31 Chain: Q
Molecule details ›
Chain: Q
Length: 120 amino acids
Theoretical weight: 13.89 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3Y3V5 (Residues: 1-120; Coverage: 100%)
Gene names: LOC107771890, LOC107792531
Sequence domains: Ribosomal protein L31e
60S ribosomal protein L32-1 Chain: R
Molecule details ›
Chain: R
Length: 133 amino acids
Theoretical weight: 15.67 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3Z2X4 (Residues: 1-133; Coverage: 100%)
Gene names: LOC107782359, LOC107785823
Sequence domains: Ribosomal protein L32
60S ribosomal protein L35a-3 Chain: S
Molecule details ›
Chain: S
Length: 112 amino acids
Theoretical weight: 12.96 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3XU79 (Residues: 1-112; Coverage: 100%)
Gene names: LOC107768641, LOC107779239, LOC107815581
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein eL34 Chain: T
Molecule details ›
Chain: T
Length: 120 amino acids
Theoretical weight: 13.79 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: P41098 (Residues: 1-120; Coverage: 100%)
Gene name: RPL34
Sequence domains: Ribosomal protein L34e
60S ribosomal protein L36 Chain: U
Molecule details ›
Chain: U
Length: 110 amino acids
Theoretical weight: 12.36 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4D2I2 (Residues: 1-110; Coverage: 100%)
Gene name: LOC107825165
Sequence domains: Ribosomal protein L36e
Ribosomal protein L37 Chain: V
Molecule details ›
Chain: V
Length: 95 amino acids
Theoretical weight: 10.88 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4DN51 (Residues: 1-95; Coverage: 100%)
Gene names: LOC107784204, LOC107831585, LOC107832335
Sequence domains: Ribosomal protein L37e
60S ribosomal protein L38 Chain: W
Molecule details ›
Chain: W
Length: 69 amino acids
Theoretical weight: 8.1 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4C4G8 (Residues: 1-69; Coverage: 100%)
Gene names: LOC107767504, LOC107815038
Sequence domains: Ribosomal L38e protein family
60S ribosomal protein L39-3 Chain: X
Molecule details ›
Chain: X
Length: 51 amino acids
Theoretical weight: 6.5 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3YR32 (Residues: 1-51; Coverage: 100%)
Gene names: LOC107774666, LOC107778797, LOC107781601, LOC107813331, LOC107814522
Sequence domains: Ribosomal L39 protein
eL40 (60S ribosomal protein L40) Chain: Y
Molecule details ›
Chain: Y
Length: 128 amino acids
Theoretical weight: 14.72 KDa
Source organism: Nicotiana tabacum
Small ribosomal subunit protein eS32 Chain: p
Molecule details ›
Chain: p
Length: 25 amino acids
Theoretical weight: 3.45 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: P62121 (Residues: 1-25; Coverage: 100%)
Gene name: RPL41
Sequence domains: Ribosomal protein L41
60S ribosomal protein L44 Chain: Z
Molecule details ›
Chain: Z
Length: 105 amino acids
Theoretical weight: 12.04 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4AVP7 (Residues: 1-105; Coverage: 100%)
Gene names: LOC107761379, LOC107767162, LOC107792576, LOC107795073, LOC107801799, LOC107802399, LOC107818115
Sequence domains: Ribosomal protein L44
60S ribosomal protein L37a Chain: a
Molecule details ›
Chain: a
Length: 92 amino acids
Theoretical weight: 10.28 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3X5Y9 (Residues: 1-92; Coverage: 100%)
Gene names: LOC107761416, LOC107766434, LOC107769002, LOC107772948, LOC107783422, LOC107787560, LOC107803180, LOC107806598, LOC107814281
Sequence domains: Ribosomal L37ae protein family
Large ribosomal subunit protein uL6 N-terminal domain-containing protein Chain: b
Molecule details ›
Chain: b
Length: 230 amino acids
Theoretical weight: 25.54 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4B0G2 (Residues: 1-230; Coverage: 100%)
Gene name: LOC107803255
Sequence domains:
60S ribosomal protein L7a Chain: c
Molecule details ›
Chain: c
Length: 258 amino acids
Theoretical weight: 29.43 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4D668 (Residues: 1-258; Coverage: 100%)
Gene name: LOC107826327
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
60S ribosomal protein L13a-4 Chain: d
Molecule details ›
Chain: d
Length: 206 amino acids
Theoretical weight: 23.53 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4DN49 (Residues: 1-206; Coverage: 100%)
Gene name: LOC107831576
Sequence domains: Ribosomal protein L13
60S ribosomal protein L23 Chain: e
Molecule details ›
Chain: e
Length: 140 amino acids
Theoretical weight: 15.04 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3XSQ1 (Residues: 1-140; Coverage: 100%)
Gene names: LOC107761645, LOC107768301, LOC107774008, LOC107812746
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: f
Molecule details ›
Chain: f
Length: 148 amino acids
Theoretical weight: 16.58 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4BFD5 (Residues: 1-148; Coverage: 100%)
Gene name: LOC107807693
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
60S ribosomal protein L10-like Chain: g
Molecule details ›
Chain: g
Length: 221 amino acids
Theoretical weight: 25.01 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3Z2D7 (Residues: 1-221; Coverage: 100%)
Gene name: LOC107782233
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein Chain: h
Molecule details ›
Chain: h
Length: 301 amino acids
Theoretical weight: 34.63 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3XE16 (Residues: 1-301; Coverage: 100%)
Gene name: LOC107764090
Sequence domains:
60S ribosomal protein L17-1-like Chain: j
Molecule details ›
Chain: j
Length: 175 amino acids
Theoretical weight: 20.14 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4CCH0 (Residues: 1-175; Coverage: 100%)
Gene name: LOC107817504
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: k
Molecule details ›
Chain: k
Length: 154 amino acids
Theoretical weight: 17.32 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: Q07761 (Residues: 1-154; Coverage: 100%)
Gene names: RPL23A, RPL25
Sequence domains:
KOW domain-containing protein Chain: m
Molecule details ›
Chain: m
Length: 146 amino acids
Theoretical weight: 16.75 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4DPM5 (Residues: 1-146; Coverage: 100%)
Gene name: LOC107831809
Sequence domains:
60S ribosomal protein L35-like Chain: n
Molecule details ›
Chain: n
Length: 123 amino acids
Theoretical weight: 14.35 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3WY31 (Residues: 1-123; Coverage: 100%)
Gene name: LOC107759229
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL2 C-terminal domain-containing protein Chain: o
Molecule details ›
Chain: o
Length: 260 amino acids
Theoretical weight: 28.22 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3XXQ5 (Residues: 1-260; Coverage: 100%)
Gene names: LOC107769978, LOC107827527
Sequence domains:
60S ribosomal protein L7-4-like Chain: q
Molecule details ›
Chain: q
Length: 242 amino acids
Theoretical weight: 28.15 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4A5Z2 (Residues: 1-242; Coverage: 100%)
Gene name: LOC107794124
Sequence domains:
60S ribosomal protein L3 Chain: r
Molecule details ›
Chain: r
Length: 389 amino acids
Theoretical weight: 44.51 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3ZLI9 (Residues: 1-389; Coverage: 100%)
Gene name: LOC107788247
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 C-terminal domain-containing protein Chain: s
Molecule details ›
Chain: s
Length: 405 amino acids
Theoretical weight: 44.71 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3X0M5 (Residues: 1-405; Coverage: 100%)
Gene name: LOC107759872
Sequence domains:
60S ribosomal protein L11-1 Chain: t
Molecule details ›
Chain: t
Length: 181 amino acids
Theoretical weight: 20.79 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S3XAW1 (Residues: 1-181; Coverage: 100%)
Gene name: LOC107763118
Sequence domains:
Large ribosomal subunit protein uL6 alpha-beta domain-containing protein Chain: u
Molecule details ›
Chain: u
Length: 194 amino acids
Theoretical weight: 22.06 KDa
Source organism: Nicotiana tabacum
UniProt:
  • Canonical: A0A1S4C068 (Residues: 1-194; Coverage: 100%)
Gene names: LOC107767112, LOC107813756
Sequence domains: Ribosomal protein L6
nascent chain Chain: l
Molecule details ›
Chain: l
Length: 24 amino acids
Theoretical weight: 2.06 KDa
Source organism: Nicotiana tabacum
5S ribosomal RNA Chain: C
Molecule details ›
Chain: C
Length: 119 nucleotides
Theoretical weight: 38.33 KDa
Sequence domains: 5S ribosomal RNA
25S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 3390 nucleotides
Theoretical weight: 1098.27 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5.8S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 163 nucleotides
Theoretical weight: 52.56 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

5 bound ligands:
Ligand MG 60 x MG
Ligand K 94 x K
Ligand ZN 4 x ZN
Ligand SPD 1 x SPD
Ligand SPM 2 x SPM
8 modified residues:
Ligand PSU 54 x PSU
Ligand OMC 16 x OMC
Ligand OMU 19 x OMU
Ligand OMG 21 x OMG
Ligand A2M 20 x A2M
Ligand 1MA 1 x 1MA
Ligand 5MC 2 x 5MC
Ligand UR3 1 x UR3

Experiments and Validation Details

Entry percentile scores
Resolution: 2.14Å
Relevant EMDB volumes: EMD-15773

Quick links

Citations

5 citation in other articles

Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes.
Mishra et al. (2024)
4 more