› 7bt6

Electron Microscopy
3.12Å resolution

Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1)

Released:
DOI: 10.2210/pdb7bt6/pdb
PDB entry 7bt6 coloured by chain, front view.
PDB entry 7bt6 coloured by chain, side view.
PDB entry 7bt6 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structural insights into assembly of the ribosomal nascent polypeptide exit tunnel.
Wilson DM, Li Y, LaPeruta A, Gamalinda M, Gao N, Woolford JL
OpenAccess logo Nat Commun 11 5111 (2020)
PMID: 33037216
Related structures: EMD-30170

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 47-mer (preferred)
PDBe Complex ID:
PDB-CPX-135797 (preferred)
Entry contents:
44 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (47 distinct):
Large ribosomal subunit protein uL2A Chain: A
Molecule details ›
Chain: A
Length: 254 amino acids
Theoretical weight: 27.46 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX45 (Residues: 1-254; Coverage: 100%)
Gene names: RPL2A, RPL5B, YFR031BC, YFR031C-A
Sequence domains:
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 387 amino acids
Theoretical weight: 43.85 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P14126 (Residues: 1-387; Coverage: 100%)
Gene names: MAK8, RPL3, TCM1, YOR063W, YOR29-14
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4A Chain: C
Molecule details ›
Chain: C
Length: 362 amino acids
Theoretical weight: 39.16 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P10664 (Residues: 1-362; Coverage: 100%)
Gene names: RPL2, RPL2A, RPL4A, YBR0315, YBR031W
Sequence domains:
Large ribosomal subunit protein uL18 Chain: D
Molecule details ›
Chain: D
Length: 297 amino acids
Theoretical weight: 33.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P26321 (Residues: 1-297; Coverage: 100%)
Gene names: LPI14W, RPL1, RPL1A, RPL5, YPL131W
Sequence domains:
Large ribosomal subunit protein eL6A Chain: E
Molecule details ›
Chain: E
Length: 176 amino acids
Theoretical weight: 20 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02326 (Residues: 1-176; Coverage: 100%)
Gene names: RPL17A, RPL6A, YL16A, YML073C
Sequence domains: Ribosomal protein L6e
Large ribosomal subunit protein uL30A Chain: F
Molecule details ›
Chain: F
Length: 244 amino acids
Theoretical weight: 27.69 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05737 (Residues: 1-244; Coverage: 100%)
Gene names: RPL6A, RPL7A, RPL8A, YGL076C, YL8A
Sequence domains:
Large ribosomal subunit protein eL8A Chain: G
Molecule details ›
Chain: G
Length: 256 amino acids
Theoretical weight: 28.18 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P17076 (Residues: 1-256; Coverage: 100%)
Gene names: MAK7, RPL4A, RPL8A, YHL033C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein uL6A Chain: H
Molecule details ›
Chain: H
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05738 (Residues: 1-191; Coverage: 100%)
Gene names: RPL8A, RPL9, RPL9A, YGL147C
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL5A Chain: J
Molecule details ›
Chain: J
Length: 174 amino acids
Theoretical weight: 19.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C0W9 (Residues: 1-174; Coverage: 100%)
Gene names: P8283.14, RP39A, RPL11A, RPL16A, YPR102C
Sequence domains:
Large ribosomal subunit protein eL13A Chain: L
Molecule details ›
Chain: L
Length: 199 amino acids
Theoretical weight: 22.6 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12690 (Residues: 1-199; Coverage: 100%)
Gene names: RPL13A, YDL082W
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14A Chain: M
Molecule details ›
Chain: M
Length: 138 amino acids
Theoretical weight: 15.2 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P36105 (Residues: 1-138; Coverage: 100%)
Gene names: RPL14A, YKL006W, YKL153
Sequence domains:
Large ribosomal subunit protein eL15A Chain: N
Molecule details ›
Chain: N
Length: 204 amino acids
Theoretical weight: 24.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05748 (Residues: 1-204; Coverage: 100%)
Gene names: RPL10A, RPL13A, RPL15A, YL10A, YLR029C
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL13A Chain: O
Molecule details ›
Chain: O
Length: 199 amino acids
Theoretical weight: 22.25 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P26784 (Residues: 1-199; Coverage: 100%)
Gene names: RPL13, RPL16A, RPL21A, YIL133C
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL22A Chain: P
Molecule details ›
Chain: P
Length: 184 amino acids
Theoretical weight: 20.59 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05740 (Residues: 1-184; Coverage: 100%)
Gene names: RPL17, RPL17A, RPL20A, YKL180W
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL18A Chain: Q
Molecule details ›
Chain: Q
Length: 186 amino acids
Theoretical weight: 20.61 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX49 (Residues: 1-186; Coverage: 100%)
Gene names: RP28A, RPL18A, YOL120C
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL19A Chain: R
Molecule details ›
Chain: R
Length: 189 amino acids
Theoretical weight: 21.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX82 (Residues: 1-189; Coverage: 100%)
Gene names: RPL19A, RPL23A, YBR084BC, YBR084C-A, YL14A
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein eL20A Chain: S
Molecule details ›
Chain: S
Length: 172 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX23 (Residues: 1-172; Coverage: 100%)
Gene names: RPL18A, RPL18A2, RPL20A, YM9408.04C, YMR242C
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein eL21A Chain: T
Molecule details ›
Chain: T
Length: 160 amino acids
Theoretical weight: 18.28 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02753 (Residues: 1-160; Coverage: 100%)
Gene names: RPL21A, URP1, YBR1401, YBR191W
Sequence domains: Ribosomal protein L21e
Large ribosomal subunit protein eL22A Chain: U
Molecule details ›
Chain: U
Length: 121 amino acids
Theoretical weight: 13.71 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05749 (Residues: 1-121; Coverage: 100%)
Gene names: L2168, RPL22A, YLR061W
Sequence domains: Ribosomal L22e protein family
Large ribosomal subunit protein uL14A Chain: V
Molecule details ›
Chain: V
Length: 137 amino acids
Theoretical weight: 14.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX41 (Residues: 1-137; Coverage: 100%)
Gene names: RPL17A, RPL17AA, RPL23A, YBL0713, YBL087C
Sequence domains: Ribosomal protein L14p/L23e
Ribosome assembly factor MRT4 Chain: W
Molecule details ›
Chain: W
Length: 236 amino acids
Theoretical weight: 27.1 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33201 (Residues: 1-236; Coverage: 100%)
Gene names: MRT4, YKL009W, YKL160
Sequence domains:
Large ribosomal subunit protein uL23 Chain: X
Molecule details ›
Chain: X
Length: 142 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04456 (Residues: 1-142; Coverage: 100%)
Gene names: RPL25, YOL127W
Sequence domains:
Large ribosomal subunit protein uL24A Chain: Y
Molecule details ›
Chain: Y
Length: 127 amino acids
Theoretical weight: 14.27 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05743 (Residues: 1-127; Coverage: 100%)
Gene names: L8300.4, RPL26, RPL26A, RPL33A, YLR344W
Sequence domains:
Large ribosomal subunit protein eL27A Chain: Z
Molecule details ›
Chain: Z
Length: 136 amino acids
Theoretical weight: 15.57 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C2H6 (Residues: 1-136; Coverage: 100%)
Gene names: RPL27, RPL27A, YHR010W
Sequence domains: Ribosomal L27e protein family
Large ribosomal subunit protein uL15 Chain: a
Molecule details ›
Chain: a
Length: 149 amino acids
Theoretical weight: 16.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P02406 (Residues: 1-149; Coverage: 100%)
Gene names: CYH2, RPL28, YGL103W
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Nucleolar GTP-binding protein 1 Chain: b
Molecule details ›
Chain: b
Length: 647 amino acids
Theoretical weight: 74.53 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02892 (Residues: 1-647; Coverage: 100%)
Gene names: LPG15W, NOG1, YPL093W
Sequence domains:
Large ribosomal subunit protein eL30 Chain: c
Molecule details ›
Chain: c
Length: 105 amino acids
Theoretical weight: 11.43 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P14120 (Residues: 1-105; Coverage: 100%)
Gene names: RPL30, RPL32, YGL030W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL31A Chain: d
Molecule details ›
Chain: d
Length: 113 amino acids
Theoretical weight: 12.98 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C2H8 (Residues: 1-113; Coverage: 100%)
Gene names: D2478, RPL31A, RPL34, RPL34A, YDL075W
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein eL32 Chain: e
Molecule details ›
Chain: e
Length: 130 amino acids
Theoretical weight: 14.81 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38061 (Residues: 1-130; Coverage: 100%)
Gene names: RPL32, YBL0838, YBL092W
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL33A Chain: f
Molecule details ›
Chain: f
Length: 107 amino acids
Theoretical weight: 12.18 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05744 (Residues: 1-107; Coverage: 100%)
Gene names: LPI4W, P2625, RPL33A, RPL37A, YPL143W
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein eL34A Chain: g
Molecule details ›
Chain: g
Length: 121 amino acids
Theoretical weight: 13.67 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P87262 (Residues: 1-121; Coverage: 100%)
Gene names: RPL34A, YER056BC, YER056C-A
Sequence domains: Ribosomal protein L34e
Large ribosomal subunit protein uL29A Chain: h
Molecule details ›
Chain: h
Length: 120 amino acids
Theoretical weight: 13.94 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX84 (Residues: 1-120; Coverage: 100%)
Gene names: D1249, RPL35A, SOS1, YDL191W
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL36A Chain: i
Molecule details ›
Chain: i
Length: 100 amino acids
Theoretical weight: 11.15 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05745 (Residues: 1-100; Coverage: 100%)
Gene names: RPL36A, RPL39A, YM9646.06, YMR194W
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL37A Chain: j
Molecule details ›
Chain: j
Length: 88 amino acids
Theoretical weight: 9.88 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P49166 (Residues: 1-88; Coverage: 100%)
Gene names: L9470.6, RPL35A, RPL37A, YLR185W
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein eL38 Chain: k
Molecule details ›
Chain: k
Length: 78 amino acids
Theoretical weight: 8.85 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P49167 (Residues: 1-78; Coverage: 100%)
Gene names: L8543.2, RPL38, YLR325C
Sequence domains: Ribosomal L38e protein family
Nucleolar GTP-binding protein 2 Chain: m
Molecule details ›
Chain: m
Length: 486 amino acids
Theoretical weight: 55.59 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53742 (Residues: 1-486; Coverage: 100%)
Gene names: N3484, NOG2, YNR053C
Sequence domains:
Large ribosomal subunit protein eL43A Chain: p
Molecule details ›
Chain: p
Length: 92 amino acids
Theoretical weight: 10.11 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX25 (Residues: 1-92; Coverage: 100%)
Gene names: RPL43A, YP9499.02, YPR043W
Sequence domains: Ribosomal L37ae protein family
Ribosome biogenesis protein NSA2 Chain: r
Molecule details ›
Chain: r
Length: 261 amino acids
Theoretical weight: 29.79 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40078 (Residues: 1-261; Coverage: 100%)
Gene names: NSA2, SYGP-ORF47, YER126C
Sequence domains: Ribosomal protein S8e
Ribosome biogenesis protein RLP24 Chain: u
Molecule details ›
Chain: u
Length: 199 amino acids
Theoretical weight: 24.03 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q07915 (Residues: 1-199; Coverage: 100%)
Gene names: RLP24, YLR009W
Sequence domains: Ribosomal protein L24e
Ribosome biogenesis protein RPF2 Chain: v
Molecule details ›
Chain: v
Length: 344 amino acids
Theoretical weight: 39.67 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P36160 (Residues: 1-344; Coverage: 100%)
Gene names: RPF2, YKR081C, YKR401
Sequence domains: Brix domain
Regulator of ribosome biosynthesis Chain: w
Molecule details ›
Chain: w
Length: 203 amino acids
Theoretical weight: 23 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08746 (Residues: 1-203; Coverage: 100%)
Gene names: RRS1, YOR294W
Sequence domains: Ribosome biogenesis regulatory protein (RRS1)
Ribosome assembly protein 4 Chain: x
Molecule details ›
Chain: x
Length: 515 amino acids
Theoretical weight: 57.11 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25382 (Residues: 1-515; Coverage: 100%)
Gene names: RSA4, YCR072C, YCR72C
Sequence domains:
Eukaryotic translation initiation factor 6 Chain: y
Molecule details ›
Chain: y
Length: 245 amino acids
Theoretical weight: 26.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12522 (Residues: 1-245; Coverage: 100%)
Gene names: CDC95, LPZ15C, TIF6, YPR016C
Sequence domains: eIF-6 family
UPF0642 protein YBL028C Chain: z
Molecule details ›
Chain: z
Length: 106 amino acids
Theoretical weight: 12.44 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38202 (Residues: 1-106; Coverage: 100%)
Gene names: YBL028C, YBL0423
Sequence domains: YBL028C ribosome biogenesis factor, N-terminal domain
RDN25-1 rRNA Chain: 1
Molecule details ›
Chain: 1
Length: 3396 nucleotides
Theoretical weight: 1097.49 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
RDN5.8-1 rRNA Chain: 2
Molecule details ›
Chain: 2
Length: 158 nucleotides
Theoretical weight: 50.68 KDa
Sequence domains: 5.8S ribosomal RNA
RDN5-2 rRNA Chain: 3
Molecule details ›
Chain: 3
Length: 121 nucleotides
Theoretical weight: 38.95 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand GTP 2 x GTP
Ligand MG 2 x MG
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.12Å
Relevant EMDB volumes: EMD-30170

Quick links

Citations

3 review citations

Quality control ensures fidelity in ribosome assembly and cellular health.
Parker et al. (2023)
2 more