› 6lsr

Electron Microscopy
3.13Å resolution

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

Released:
DOI: 10.2210/pdb6lsr/pdb
PDB entry 6lsr coloured by chain, front view.
PDB entry 6lsr coloured by chain, side view.
PDB entry 6lsr coloured by chain, top view.
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-0963

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 48-mer (preferred)
PDBe Complex ID:
PDB-CPX-148286 (preferred)
Entry contents:
45 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (48 distinct):
Cytoplasmic 60S subunit biogenesis factor ZNF622 Chain: 0
Molecule details ›
Chain: 0
Length: 477 amino acids
Theoretical weight: 54.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q969S3 (Residues: 1-477; Coverage: 100%)
Gene names: ZNF622, ZPR9
Sequence domains:
Large subunit GTPase 1 homolog Chain: 1
Molecule details ›
Chain: 1
Length: 658 amino acids
Theoretical weight: 75.34 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H089 (Residues: 1-658; Coverage: 100%)
Gene name: LSG1
Sequence domains: 50S ribosome-binding GTPase
60S ribosomal export protein NMD3 Chain: 3
Molecule details ›
Chain: 3
Length: 534 amino acids
Theoretical weight: 61.4 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q96D46 (Residues: 1-503; Coverage: 100%)
Gene names: CGI-07, NMD3
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
Large ribosomal subunit protein uL1 Chain: A
Molecule details ›
Chain: A
Length: 217 amino acids
Theoretical weight: 24.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62906 (Residues: 1-217; Coverage: 100%)
Gene names: NEDD6, RPL10A
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL3 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
Large ribosomal subunit protein eL29 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
Sequence domains: Ribosomal L29e protein family
Large ribosomal subunit protein uL4 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:
Large ribosomal subunit protein eL30 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
Large ribosomal subunit protein eL34 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
Large ribosomal subunit protein eL8 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
Large ribosomal subunit protein uL29 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
Large ribosomal subunit protein uL6 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
Large ribosomal subunit protein eL36 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
Large ribosomal subunit protein uL15 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
Large ribosomal subunit protein eL37 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
Large ribosomal subunit protein uL5 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:
Large ribosomal subunit protein eL38 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
Large ribosomal subunit protein eL39 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
Sequence domains: Ribosomal L39 protein
Large ribosomal subunit protein eL13 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
Large ribosomal subunit protein eL14 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
Large ribosomal subunit protein eL31 Chain: T
Molecule details ›
Chain: T
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
Large ribosomal subunit protein eL15 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
Large ribosomal subunit protein uL13 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
Large ribosomal subunit protein eL42 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
Large ribosomal subunit protein eL43 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
Large ribosomal subunit protein uL22 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
Large ribosomal subunit protein eL18 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
Large ribosomal subunit protein eL19 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
Large ribosomal subunit protein eL20 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
Large ribosomal subunit protein eL21 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
Large ribosomal subunit protein eL22 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
Large ribosomal subunit protein uL14 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
Large ribosomal subunit protein eL24 Chain: f
Molecule details ›
Chain: f
Length: 157 amino acids
Theoretical weight: 17.83 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P83731 (Residues: 1-157; Coverage: 100%)
Gene name: RPL24
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL23 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:
Large ribosomal subunit protein uL24 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:
Large ribosomal subunit protein eL27 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:
Large ribosomal subunit protein eL28 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
Large ribosomal subunit protein uL2 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:
Large ribosomal subunit protein uL18 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:
Large ribosomal subunit protein eL32 Chain: t
Molecule details ›
Chain: t
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
Large ribosomal subunit protein eL33 Chain: u
Molecule details ›
Chain: u
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
Large ribosomal subunit protein eL6 Chain: v
Molecule details ›
Chain: v
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:
Large ribosomal subunit protein uL30 Chain: w
Molecule details ›
Chain: w
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:
Proliferation-associated protein 2G4 Chain: z
Molecule details ›
Chain: z
Length: 394 amino acids
Theoretical weight: 43.85 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UQ80 (Residues: 1-394; Coverage: 100%)
Gene names: EBP1, PA2G4
Sequence domains: Metallopeptidase family M24
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
5.8S ribosomal RNA Chain: 8
Molecule details ›
Chain: 8
Length: 156 nucleotides
Theoretical weight: 50.14 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand MG 246 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 14 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 2 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: 3.13Å
Relevant EMDB volumes: EMD-0963
Expression system: Homo sapiens

Quick links

Citations

3 review citations

Ribosomal Protein L10: From Function to Dysfunction.
Pollutri et al. (2020)
2 more

3 mentions without citation

Ribosome biogenesis factors-from names to functions.
Dörner et al. (2023)
2 more