› 6lss

Electron Microscopy
3.23Å resolution

Cryo-EM structure of a pre-60S ribosomal subunit - state preA

Released:
DOI: 10.2210/pdb6lss/pdb
PDB 6lss coloured by chain and viewed from the front.
PDB 6lss coloured by chain and viewed from the side.
PDB 6lss coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
Structural snapshots of human pre-60S ribosomal particles before and after nuclear export.
Liang X, Zuo MQ, Zhang Y, Li N, Ma C, Dong MQ, Gao N
Nat Commun 11 3542 (2020)
PMID: 32669547
Related structures: EMD-0964

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 48-mer (preferred)
Entry contents:
45 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (48 distinct):
Nucleolar GTP-binding protein 2 Chain: 1
Molecule details ›
Chain: 1
Length: 731 amino acids
Theoretical weight: 83.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13823 (Residues: 1-731; Coverage: 100%)
Gene names: GNL2, NGP1
Sequence domains:
GTP-binding protein 4 Chain: 4
Molecule details ›
Chain: 4
Length: 634 amino acids
Theoretical weight: 74.11 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BZE4 (Residues: 1-634; Coverage: 100%)
Gene names: CRFG, GTPBP4, NOG1
Sequence domains:
Eukaryotic translation initiation factor 6 Chain: 6
Molecule details ›
Chain: 6
Length: 245 amino acids
Theoretical weight: 26.62 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P56537 (Residues: 1-245; Coverage: 100%)
Gene names: EIF3A, EIF6, ITGB4BP, OK/SW-cl.27
Sequence domains: eIF-6 family
Probable ribosome biogenesis protein RLP24 Chain: 7
Molecule details ›
Chain: 7
Length: 163 amino acids
Theoretical weight: 19.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UHA3 (Residues: 1-163; Coverage: 100%)
Gene names: C15orf15, My024, RPL24L, RSL24D1
Sequence domains: Ribosomal protein L24e
Zinc finger protein 593 Chain: 9
Molecule details ›
Chain: 9
Length: 134 amino acids
Theoretical weight: 15.23 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00488 (Residues: 1-134; Coverage: 100%)
Gene names: ZNF593, ZT86
60S ribosomal protein L3 Chain: B
Molecule details ›
Chain: B
Length: 403 amino acids
Theoretical weight: 46.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39023 (Residues: 1-403; Coverage: 100%)
Gene names: OK/SW-cl.32, RPL3
Sequence domains: Ribosomal protein L3
60S ribosomal protein L29 Chain: C
Molecule details ›
Chain: C
Length: 159 amino acids
Theoretical weight: 17.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P47914 (Residues: 1-159; Coverage: 100%)
Gene name: RPL29
60S ribosomal protein L4 Chain: D
Molecule details ›
Chain: D
Length: 427 amino acids
Theoretical weight: 47.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P36578 (Residues: 1-427; Coverage: 100%)
Gene names: RPL1, RPL4
Sequence domains:
60S ribosomal protein L30 Chain: E
Molecule details ›
Chain: E
Length: 115 amino acids
Theoretical weight: 12.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62888 (Residues: 1-115; Coverage: 100%)
Gene name: RPL30
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
60S ribosomal protein L34 Chain: F
Molecule details ›
Chain: F
Length: 117 amino acids
Theoretical weight: 13.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49207 (Residues: 1-117; Coverage: 100%)
Gene name: RPL34
Sequence domains: Ribosomal protein L34e
60S ribosomal protein L7a Chain: G
Molecule details ›
Chain: G
Length: 266 amino acids
Theoretical weight: 30.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62424 (Residues: 1-266; Coverage: 100%)
Gene names: RPL7A, SURF-3, SURF3
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
60S ribosomal protein L35 Chain: H
Molecule details ›
Chain: H
Length: 123 amino acids
Theoretical weight: 14.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P42766 (Residues: 1-123; Coverage: 100%)
Gene name: RPL35
Sequence domains: Ribosomal L29 protein
60S ribosomal protein L9 Chain: I
Molecule details ›
Chain: I
Length: 192 amino acids
Theoretical weight: 21.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P32969 (Residues: 1-192; Coverage: 100%)
Gene names: OK/SW-cl.103, RPL9, RPL9P7, RPL9P8, RPL9P9
Sequence domains: Ribosomal protein L6
60S ribosomal protein L36 Chain: K
Molecule details ›
Chain: K
Length: 105 amino acids
Theoretical weight: 12.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3U8 (Residues: 1-105; Coverage: 100%)
Gene name: RPL36
Sequence domains: Ribosomal protein L36e
60S ribosomal protein L27a Chain: L
Molecule details ›
Chain: L
Length: 148 amino acids
Theoretical weight: 16.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46776 (Residues: 1-148; Coverage: 100%)
Gene name: RPL27A
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
60S ribosomal protein L37 Chain: M
Molecule details ›
Chain: M
Length: 97 amino acids
Theoretical weight: 11.11 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61927 (Residues: 1-97; Coverage: 100%)
Gene name: RPL37
Sequence domains: Ribosomal protein L37e
60S ribosomal protein L11 Chain: N
Molecule details ›
Chain: N
Length: 178 amino acids
Theoretical weight: 20.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62913 (Residues: 1-178; Coverage: 100%)
Gene name: RPL11
Sequence domains:
60S ribosomal protein L38 Chain: O
Molecule details ›
Chain: O
Length: 70 amino acids
Theoretical weight: 8.24 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63173 (Residues: 1-70; Coverage: 100%)
Gene name: RPL38
Sequence domains: Ribosomal L38e protein family
60S ribosomal protein L39 Chain: P
Molecule details ›
Chain: P
Length: 51 amino acids
Theoretical weight: 6.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62891 (Residues: 1-51; Coverage: 100%)
Gene name: RPL39
60S ribosomal protein L13 Chain: Q
Molecule details ›
Chain: Q
Length: 211 amino acids
Theoretical weight: 24.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P26373 (Residues: 1-211; Coverage: 100%)
Gene names: BBC1, OK/SW-cl.46, RPL13
Sequence domains: Ribosomal protein L13e
Translation machinery-associated protein 16 Chain: R
Molecule details ›
Chain: R
Length: 203 amino acids
Theoretical weight: 23.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96EY4 (Residues: 1-203; Coverage: 100%)
Gene names: C4orf43, TMA16
Sequence domains: Translation machinery-associated protein 16
60S ribosomal protein L14 Chain: S
Molecule details ›
Chain: S
Length: 215 amino acids
Theoretical weight: 23.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P50914 (Residues: 1-215; Coverage: 100%)
Gene name: RPL14
Sequence domains: Ribosomal protein L14
60S ribosomal protein L15 Chain: U
Molecule details ›
Chain: U
Length: 204 amino acids
Theoretical weight: 24.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61313 (Residues: 1-204; Coverage: 100%)
Gene names: EC45, RPL15, TCBAP0781
Sequence domains: Ribosomal L15
60S ribosomal protein L13a Chain: V
Molecule details ›
Chain: V
Length: 203 amino acids
Theoretical weight: 23.63 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P40429 (Residues: 1-203; Coverage: 100%)
Gene name: RPL13A
Sequence domains: Ribosomal protein L13
60S ribosomal protein L36a Chain: W
Molecule details ›
Chain: W
Length: 106 amino acids
Theoretical weight: 12.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P83881 (Residues: 1-106; Coverage: 100%)
Gene names: GIG15, MIG6, RPL36A, RPL44
Sequence domains: Ribosomal protein L44
60S ribosomal protein L37a Chain: X
Molecule details ›
Chain: X
Length: 92 amino acids
Theoretical weight: 10.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61513 (Residues: 1-92; Coverage: 100%)
Gene name: RPL37A
Sequence domains: Ribosomal L37ae protein family
60S ribosomal protein L17 Chain: Y
Molecule details ›
Chain: Y
Length: 184 amino acids
Theoretical weight: 21.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P18621 (Residues: 1-184; Coverage: 100%)
Gene name: RPL17
Sequence domains: Ribosomal protein L22p/L17e
60S ribosomal protein L18 Chain: Z
Molecule details ›
Chain: Z
Length: 188 amino acids
Theoretical weight: 21.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q07020 (Residues: 1-188; Coverage: 100%)
Gene name: RPL18
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
60S ribosomal protein L19 Chain: a
Molecule details ›
Chain: a
Length: 196 amino acids
Theoretical weight: 23.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P84098 (Residues: 1-196; Coverage: 100%)
Gene name: RPL19
Sequence domains: Ribosomal protein L19e
60S ribosomal protein L18a Chain: b
Molecule details ›
Chain: b
Length: 176 amino acids
Theoretical weight: 20.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q02543 (Residues: 1-176; Coverage: 100%)
Gene name: RPL18A
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
60S ribosomal protein L21 Chain: c
Molecule details ›
Chain: c
Length: 160 amino acids
Theoretical weight: 18.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46778 (Residues: 1-160; Coverage: 100%)
Gene name: RPL21
Sequence domains: Ribosomal protein L21e
60S ribosomal protein L22 Chain: d
Molecule details ›
Chain: d
Length: 128 amino acids
Theoretical weight: 14.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P35268 (Residues: 1-128; Coverage: 100%)
Gene name: RPL22
Sequence domains: Ribosomal L22e protein family
60S ribosomal protein L23 Chain: e
Molecule details ›
Chain: e
Length: 140 amino acids
Theoretical weight: 14.89 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62829 (Residues: 1-140; Coverage: 100%)
Gene name: RPL23
Sequence domains: Ribosomal protein L14p/L23e
60S ribosomal protein L23a Chain: g
Molecule details ›
Chain: g
Length: 156 amino acids
Theoretical weight: 17.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62750 (Residues: 1-156; Coverage: 100%)
Gene name: RPL23A
Sequence domains:
60S ribosomal protein L26 Chain: h
Molecule details ›
Chain: h
Length: 145 amino acids
Theoretical weight: 17.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61254 (Residues: 1-145; Coverage: 100%)
Gene name: RPL26
Sequence domains: Ribosomal proteins L26 eukaryotic, L24P archaeal
60S ribosomal protein L27 Chain: i
Molecule details ›
Chain: i
Length: 136 amino acids
Theoretical weight: 15.84 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61353 (Residues: 1-136; Coverage: 100%)
Gene name: RPL27
Sequence domains: Ribosomal L27e protein family
60S ribosomal protein L31 Chain: j
Molecule details ›
Chain: j
Length: 125 amino acids
Theoretical weight: 14.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62899 (Residues: 1-125; Coverage: 100%)
Gene name: RPL31
Sequence domains: Ribosomal protein L31e
60S ribosomal protein L32 Chain: k
Molecule details ›
Chain: k
Length: 135 amino acids
Theoretical weight: 15.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62910 (Residues: 1-135; Coverage: 100%)
Gene names: PP9932, RPL32
Sequence domains: Ribosomal protein L32
60S ribosomal protein L28 Chain: l
Molecule details ›
Chain: l
Length: 137 amino acids
Theoretical weight: 15.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46779 (Residues: 1-137; Coverage: 100%)
Gene name: RPL28
Sequence domains: Ribosomal L28e protein family
60S ribosomal protein L8 Chain: m
Molecule details ›
Chain: m
Length: 257 amino acids
Theoretical weight: 28.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62917 (Residues: 1-257; Coverage: 100%)
Gene name: RPL8
Sequence domains:
60S ribosomal protein L35a Chain: n
Molecule details ›
Chain: n
Length: 110 amino acids
Theoretical weight: 12.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P18077 (Residues: 1-110; Coverage: 100%)
Gene names: GIG33, RPL35A
Sequence domains: Ribosomal protein L35Ae
60S ribosomal protein L6 Chain: o
Molecule details ›
Chain: o
Length: 288 amino acids
Theoretical weight: 32.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q02878 (Residues: 1-288; Coverage: 100%)
Gene names: RPL6, TXREB1
Sequence domains:
60S ribosomal protein L7 Chain: p
Molecule details ›
Chain: p
Length: 248 amino acids
Theoretical weight: 29.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P18124 (Residues: 1-248; Coverage: 100%)
Gene name: RPL7
Sequence domains:
60S ribosomal protein L5 Chain: r
Molecule details ›
Chain: r
Length: 297 amino acids
Theoretical weight: 34.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46777 (Residues: 1-297; Coverage: 100%)
Gene names: MSTP030, RPL5
Sequence domains:
Protein LLP homolog Chain: z
Molecule details ›
Chain: z
Length: 129 amino acids
Theoretical weight: 15.27 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BRT6 (Residues: 1-129; Coverage: 100%)
Gene names: C12orf31, LLPH, cPERP-G
Sequence domains: Learning-associated protein
28S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 5070 nucleotides
Theoretical weight: 1641.89 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chain: 5
Molecule details ›
Chain: 5
Length: 120 nucleotides
Theoretical weight: 38.69 KDa
Sequence domains: 5S ribosomal RNA
28S ribosomal RNA Chain: 8
Molecule details ›
Chain: 8
Length: 156 nucleotides
Theoretical weight: 50.16 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand MG 250 x MG
27 modified residues:
Ligand B9B 3 x B9B
Ligand OMG 16 x OMG
Ligand A2M 14 x A2M
Ligand 2MG 4 x 2MG
Ligand 1MA 2 x 1MA
Ligand P4U 1 x P4U
Ligand B8Q 1 x B8Q
Ligand PSU 11 x PSU
Ligand 7MG 3 x 7MG
Ligand I4U 2 x I4U
Ligand E7G 2 x E7G
Ligand B8H 2 x B8H
Ligand UR3 3 x UR3
Ligand P7G 2 x P7G
Ligand OMC 9 x OMC
Ligand B8W 5 x B8W
Ligand B9H 1 x B9H
Ligand 5MC 3 x 5MC
Ligand B8K 2 x B8K
Ligand BGH 1 x BGH
Ligand 5MU 1 x 5MU
Ligand 6MZ 1 x 6MZ
Ligand OMU 3 x OMU
Ligand E6G 1 x E6G
Ligand MHG 1 x MHG
Ligand B8T 2 x B8T
Ligand M7A 1 x M7A

Experiments and Validation Details

Entry percentile scores
Resolution: 3.23Å
Relevant EMDB volumes: EMD-0964

Quick links

Citations

2 review citations

Structural overview of macromolecular machines involved in ribosome biogenesis.
Frazier et al. (2021)
1 more