› 8fkr

Electron Microscopy
2.89Å resolution

Human nucleolar pre-60S ribosomal subunit (State B1)

Released:
DOI: 10.2210/pdb8fkr/pdb
PDB entry 8fkr coloured by chain, front view.
PDB entry 8fkr coloured by chain, side view.
PDB entry 8fkr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Principles of human pre-60S biogenesis.
Vanden Broeck A, Klinge S
Science 381 eadh3892 (2023)
PMID: 37410842
Related structures: EMD-29254

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 51-mer (preferred)
PDBe Complex ID:
PDB-CPX-221152 (preferred)
Entry contents:
48 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (51 distinct):
Large ribosomal subunit protein uL11 Chain: BA
Molecule details ›
Chain: BA
Length: 165 amino acids
Theoretical weight: 17.85 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P30050 (Residues: 1-165; Coverage: 100%)
Gene name: RPL12
Sequence domains:
Large ribosomal subunit protein eL13 Chain: L6
Molecule details ›
Chain: L6
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 uL13 Chain: L7
Molecule details ›
Chain: L7
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 eL14 Chain: L8
Molecule details ›
Chain: L8
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 eL15 Chain: L9
Molecule details ›
Chain: L9
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 uL22 Chain: LA
Molecule details ›
Chain: LA
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: LB
Molecule details ›
Chain: LB
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 eL20 Chain: LC
Molecule details ›
Chain: LC
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: LE
Molecule details ›
Chain: LE
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 uL14 Chain: LG
Molecule details ›
Chain: LG
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 uL23 Chain: LH
Molecule details ›
Chain: LH
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: LI
Molecule details ›
Chain: LI
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 uL15 Chain: LK
Molecule details ›
Chain: LK
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 uL3 Chain: LN
Molecule details ›
Chain: LN
Length: 403 amino acids
Theoretical weight: 46.22 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 eL32 Chain: LQ
Molecule details ›
Chain: LQ
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 uL29 Chain: LS
Molecule details ›
Chain: LS
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 eL33 Chain: LT
Molecule details ›
Chain: LT
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 eL36 Chain: LU
Molecule details ›
Chain: LU
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 eL37 Chain: LW
Molecule details ›
Chain: LW
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
Guanine nucleotide-binding protein-like 3 Chain: NB
Molecule details ›
Chain: NB
Length: 549 amino acids
Theoretical weight: 62.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BVP2 (Residues: 1-549; Coverage: 100%)
Gene names: E2IG3, GNL3, NS
Sequence domains:
Surfeit locus protein 6 Chain: NE
Molecule details ›
Chain: NE
Length: 361 amino acids
Theoretical weight: 41.55 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75683 (Residues: 1-361; Coverage: 100%)
Gene names: SURF-6, SURF6
Sequence domains: Surfeit locus protein 6
Ribosome biogenesis protein NSA2 homolog Chain: NF
Molecule details ›
Chain: NF
Length: 260 amino acids
Theoretical weight: 30.14 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95478 (Residues: 1-260; Coverage: 100%)
Gene names: HUSSY-29, NSA2, TINP1
Sequence domains: Ribosomal protein S8e
RRP15-like protein Chain: NG
Molecule details ›
Chain: NG
Length: 282 amino acids
Theoretical weight: 31.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3B9 (Residues: 1-282; Coverage: 100%)
Gene names: CGI-115, KIAA0507, RRP15
Sequence domains: Rrp15p
Protein MAK16 homolog Chain: NM
Molecule details ›
Chain: NM
Length: 300 amino acids
Theoretical weight: 35.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BXY0 (Residues: 1-300; Coverage: 100%)
Gene names: MAK16, RBM13
Sequence domains:
Suppressor of SWI4 1 homolog Chain: NN
Molecule details ›
Chain: NN
Length: 473 amino acids
Theoretical weight: 53.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NQ55 (Residues: 1-473; Coverage: 100%)
Gene names: BXDC3, PPAN, SSF1
Sequence domains: Brix domain
Ribosomal RNA processing protein 1 homolog A Chain: NO
Molecule details ›
Chain: NO
Length: 461 amino acids
Theoretical weight: 52.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P56182 (Residues: 1-461; Coverage: 100%)
Gene names: D21S2056E, NNP1, NOP52, RRP1, RRP1A
Sequence domains: Nucleolar protein,Nop52
WD repeat-containing protein 74 Chain: NQ
Molecule details ›
Chain: NQ
Length: 385 amino acids
Theoretical weight: 42.5 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6RFH5 (Residues: 1-385; Coverage: 100%)
Gene names: NSA1, WDR74
Sequence domains: WD domain, G-beta repeat
Ribosome production factor 1 Chain: NS
Molecule details ›
Chain: NS
Length: 349 amino acids
Theoretical weight: 40.19 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H9Y2 (Residues: 1-349; Coverage: 100%)
Gene names: BXDC5, RPF1
Sequence domains: Brix domain
Large ribosomal subunit protein uL4 Chain: SA
Molecule details ›
Chain: SA
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 eL6 Chain: SC
Molecule details ›
Chain: SC
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: SD
Molecule details ›
Chain: SD
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:
Large ribosomal subunit protein eL8 Chain: SE
Molecule details ›
Chain: SE
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 uL6 Chain: SG
Molecule details ›
Chain: SG
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
MKI67 FHA domain-interacting nucleolar phosphoprotein Chain: SH
Molecule details ›
Chain: SH
Length: 293 amino acids
Theoretical weight: 34.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYG3 (Residues: 1-293; Coverage: 100%)
Gene names: MKI67IP, NIFK, NOPP34
Sequence domains:
Ribosomal protein uL30-like Chain: SI
Molecule details ›
Chain: SI
Length: 255 amino acids
Theoretical weight: 29.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6DKI1 (Residues: 1-255; Coverage: 100%)
Gene name: RPL7L1
Sequence domains:
pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 Chain: SJ
Molecule details ›
Chain: SJ
Length: 847 amino acids
Theoretical weight: 96.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8IY81 (Residues: 1-847; Coverage: 100%)
Gene names: FTSJ3, SB92
Sequence domains:
Eukaryotic translation initiation factor 6 Chain: SK
Molecule details ›
Chain: SK
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
Ribosomal L1 domain-containing protein 1 Chain: SL
Molecule details ›
Chain: SL
Length: 490 amino acids
Theoretical weight: 55.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O76021 (Residues: 1-490; Coverage: 100%)
Gene names: CATX11, CSIG, L12, PBK1, RSL1D1
Sequence domains: Ribosomal protein L1p/L10e family
Pescadillo homolog Chain: SM
Molecule details ›
Chain: SM
Length: 588 amino acids
Theoretical weight: 68.11 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00541 (Residues: 1-588; Coverage: 100%)
Gene name: PES1
Sequence domains:
Probable rRNA-processing protein EBP2 Chain: SN
Molecule details ›
Chain: SN
Length: 306 amino acids
Theoretical weight: 34.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99848 (Residues: 1-306; Coverage: 100%)
Gene names: EBNA1BP2, EBP2
Sequence domains: Eukaryotic rRNA processing protein EBP2
Ribosome biogenesis protein BRX1 homolog Chain: SO
Molecule details ›
Chain: SO
Length: 353 amino acids
Theoretical weight: 41.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8TDN6 (Residues: 1-353; Coverage: 100%)
Gene names: BRIX, BRIX1, BXDC2
Sequence domains: Brix domain
mRNA turnover protein 4 homolog Chain: SQ
Molecule details ›
Chain: SQ
Length: 239 amino acids
Theoretical weight: 27.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UKD2 (Residues: 1-239; Coverage: 100%)
Gene names: C1orf33, MRT4, MRTO4
Sequence domains:
GTP-binding protein 4 Chain: SR
Molecule details ›
Chain: SR
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:
Ribosome biogenesis protein BOP1 Chain: SS
Molecule details ›
Chain: SS
Length: 746 amino acids
Theoretical weight: 83.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q14137 (Residues: 1-746; Coverage: 100%)
Gene names: BOP1, KIAA0124
Sequence domains:
Ribosome biogenesis regulatory protein homolog Chain: ST
Molecule details ›
Chain: ST
Length: 365 amino acids
Theoretical weight: 41.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15050 (Residues: 1-365; Coverage: 100%)
Gene names: KIAA0112, RRR, RRS1
Sequence domains: Ribosome biogenesis regulatory protein (RRS1)
Probable ribosome biogenesis protein RLP24 Chain: SV
Molecule details ›
Chain: SV
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
ATP-dependent RNA helicase DDX18 Chain: SW
Molecule details ›
Chain: SW
Length: 670 amino acids
Theoretical weight: 75.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NVP1 (Residues: 1-670; Coverage: 100%)
Gene names: DDX18, cPERP-D
Sequence domains:
Nucleolar protein 16 Chain: SZ
Molecule details ›
Chain: SZ
Length: 178 amino acids
Theoretical weight: 21.23 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3C1 (Residues: 1-178; Coverage: 100%)
Gene names: CGI-117, HSPC111, NOP16
Sequence domains: Ribosome biogenesis protein Nop16
5.8S ribosomal RNA Chain: L1
Molecule details ›
Chain: L1
Length: 157 nucleotides
Theoretical weight: 50.45 KDa
Sequence domains: 5.8S ribosomal RNA
ITS2 rRNA Chain: L2
Molecule details ›
Chain: L2
Length: 1167 nucleotides
Theoretical weight: 376.43 KDa
28S ribosomal RNA Chain: L3
Molecule details ›
Chain: L3
Length: 5070 nucleotides
Theoretical weight: 1640.22 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA

Ligands and Environments

5 bound ligands:
Ligand MG 54 x MG
Ligand ZN 2 x ZN
Ligand SF4 1 x SF4
Ligand GDP 1 x GDP
Ligand K 1 x K
2 modified residues:
Ligand HIC 1 x HIC
Ligand SEP 2 x SEP

Experiments and Validation Details

Entry percentile scores
Resolution: 2.89Å
Relevant EMDB volumes: EMD-29254

Quick links

Citations

2 citation in other articles

Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Thoms et al. (2023)
1 more