Structure analysis

Human nucleolar pre-60S ribosomal subunit (State B2)

Electron Microscopy
2.88Å resolution
Source organism: Homo sapiens
Assembly composition:
hetero 47-mer (preferred)
Entry contents: 44 distinct polypeptide molecules
3 distinct RNA molecules

Assemblies

Assembly 1 (preferred)
Download    3D Visualisation
Multimeric state: hetero 47-mer
Accessible surface area: 609568.81 Å2
Buried surface area: 325512.94 Å2
Dissociation area: 2,265.19 Å2
Dissociation energy (ΔGdiss): 10.75 kcal/mol
Dissociation entropy (TΔSdiss): 15.87 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-271471

Macromolecules

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
Pfam:
PDBe-KB: UniProt Coverage View: P30050  
116520406080100120140160
 
50100150
UniProt
P30050
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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
Pfam: Ribosomal protein L13e
PDBe-KB: UniProt Coverage View: P26373  
121120406080100120140160180200
 
50100150200
UniProt
P26373
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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
Pfam: Ribosomal protein L13
PDBe-KB: UniProt Coverage View: P40429  
120320406080100120140160180200
 
50100150200
UniProt
P40429
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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
Pfam: Ribosomal protein L14
PDBe-KB: UniProt Coverage View: P50914  
121520406080100120140160180200
 
100200
UniProt
P50914
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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
Pfam: Ribosomal L15
PDBe-KB: UniProt Coverage View: P61313  
120420406080100120140160180200
 
50100150200
UniProt
P61313
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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
Pfam: Ribosomal protein L22p/L17e
PDBe-KB: UniProt Coverage View: P18621  
118420406080100120140160180
 
50100150
UniProt
P18621
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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
Pfam: Ribosomal protein 60S L18 and 50S L18e
PDBe-KB: UniProt Coverage View: Q07020  
118820406080100120140160180
 
50100150
UniProt
Q07020
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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
Pfam: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
PDBe-KB: UniProt Coverage View: Q02543  
117620406080100120140160
 
50100150
UniProt
Q02543
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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
Pfam: Ribosomal protein L21e
PDBe-KB: UniProt Coverage View: P46778  
116020406080100120140160
 
50100150
UniProt
P46778
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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
Pfam: Ribosomal protein L14p/L23e
PDBe-KB: UniProt Coverage View: P62829  
1140102030405060708090100110120130140
 
50100
UniProt
P62829
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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
Pfam:
PDBe-KB: UniProt Coverage View: P62750  
115620406080100120140
 
50100150
UniProt
P62750
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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
Pfam:
PDBe-KB: UniProt Coverage View: P61254  
114520406080100120140
 
50100
UniProt
P61254
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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
Pfam: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
PDBe-KB: UniProt Coverage View: P46776  
114820406080100120140
 
50100
UniProt
P46776
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Chain: LL
Length: 137 amino acids
Theoretical weight: 15.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46779 (Residues: 1-137; Coverage: 100%)
Gene name: RPL28
Pfam: Ribosomal L28e protein family
PDBe-KB: UniProt Coverage View: P46779  
1137102030405060708090100110120130
 
50100
UniProt
P46779
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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
Pfam: Ribosomal protein L3
PDBe-KB: UniProt Coverage View: P39023  
140350100150200250300350400
 
100200300400
UniProt
P39023
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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
Pfam: Ribosomal protein L32
PDBe-KB: UniProt Coverage View: P62910  
1135102030405060708090100110120130
 
50100
UniProt
P62910
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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
Pfam: Ribosomal L29 protein
PDBe-KB: UniProt Coverage View: P42766  
1123102030405060708090100110120
 
50100
UniProt
P42766
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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
Pfam: Ribosomal protein L35Ae
PDBe-KB: UniProt Coverage View: P18077  
1110102030405060708090100110
 
50100
UniProt
P18077
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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
Pfam: Ribosomal protein L36e
PDBe-KB: UniProt Coverage View: Q9Y3U8  
1105102030405060708090100
 
50100
UniProt
Q9Y3U8
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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
Pfam: Ribosomal protein L37e
PDBe-KB: UniProt Coverage View: P61927  
197102030405060708090
 
50
UniProt
P61927
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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
Pfam: Surfeit locus protein 6
PDBe-KB: UniProt Coverage View: O75683  
136150100150200250300350
 
100200300
UniProt
O75683
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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
Pfam: Ribosomal protein S8e
PDBe-KB: UniProt Coverage View: O95478  
126020406080100120140160180200220240260
 
100200
UniProt
O95478
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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
Pfam: Rrp15p
PDBe-KB: UniProt Coverage View: Q9Y3B9  
128220406080100120140160180200220240260280
 
100200
UniProt
Q9Y3B9
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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
Pfam: Brix domain
PDBe-KB: UniProt Coverage View: Q9NQ55  
147350100150200250300350400450
 
200400
UniProt
Q9NQ55
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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
Pfam:
PDBe-KB: UniProt Coverage View: P36578  
142750100150200250300350400
 
200400
UniProt
P36578
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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
Pfam:
PDBe-KB: UniProt Coverage View: Q02878  
128820406080100120140160180200220240260280
 
100200
UniProt
Q02878
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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
Pfam:
PDBe-KB: UniProt Coverage View: P18124  
124820406080100120140160180200220240
 
100200
UniProt
P18124
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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
Pfam: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
PDBe-KB: UniProt Coverage View: P62424  
126620406080100120140160180200220240260
 
100200
UniProt
P62424
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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
Pfam: Ribosomal protein L6
PDBe-KB: UniProt Coverage View: P32969  
119220406080100120140160180
 
50100150
UniProt
P32969
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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
Pfam:
PDBe-KB: UniProt Coverage View: Q9BYG3  
129320406080100120140160180200220240260280
 
100200
UniProt
Q9BYG3
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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
Pfam:
PDBe-KB: UniProt Coverage View: Q6DKI1  
125520406080100120140160180200220240
 
100200
UniProt
Q6DKI1
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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
Pfam:
PDBe-KB: UniProt Coverage View: Q8IY81  
1847100200300400500600700800
 
200400600800
UniProt
Q8IY81
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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
Pfam: eIF-6 family
PDBe-KB: UniProt Coverage View: P56537  
124520406080100120140160180200220240
 
100200
UniProt
P56537
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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
Pfam: Ribosomal protein L1p/L10e family
PDBe-KB: UniProt Coverage View: O76021  
149050100150200250300350400450
 
200400
UniProt
O76021
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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
Pfam:
PDBe-KB: UniProt Coverage View: O00541  
158850100150200250300350400450500550
 
200400
UniProt
O00541
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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
Pfam: Eukaryotic rRNA processing protein EBP2
PDBe-KB: UniProt Coverage View: Q99848  
130620406080100120140160180200220240260280300
 
100200300
UniProt
Q99848
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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
Pfam: Brix domain
PDBe-KB: UniProt Coverage View: Q8TDN6  
135350100150200250300350
 
100200300
UniProt
Q8TDN6
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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
Pfam:
PDBe-KB: UniProt Coverage View: Q9UKD2  
123920406080100120140160180200220
 
100200
UniProt
Q9UKD2
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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
Pfam:
PDBe-KB: UniProt Coverage View: Q9BZE4  
163450100150200250300350400450500550600
 
200400600
UniProt
Q9BZE4
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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
Pfam:
PDBe-KB: UniProt Coverage View: Q14137  
1746100200300400500600700
 
200400600
UniProt
Q14137
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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
Pfam: Ribosome biogenesis regulatory protein (RRS1)
PDBe-KB: UniProt Coverage View: Q15050  
136550100150200250300350
 
100200300
UniProt
Q15050
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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
Pfam: Ribosomal protein L24e
PDBe-KB: UniProt Coverage View: Q9UHA3  
116320406080100120140160
 
50100150
UniProt
Q9UHA3
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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
Pfam:
PDBe-KB: UniProt Coverage View: Q9NVP1  
167050100150200250300350400450500550600650
 
200400600
UniProt
Q9NVP1
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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
Pfam: Ribosome biogenesis protein Nop16
PDBe-KB: UniProt Coverage View: Q9Y3C1  
117820406080100120140160
 
50100150
UniProt
Q9Y3C1
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Name: 5.8S ribosomal RNA
Representative chains: L1
Length: 157 nucleotides
Theoretical weight: 50.45 KDa
Rfam: 5.8S ribosomal RNA
115720406080100120140
 
50100150
Chains
Chain B (auth L1)
Rfam
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Name: ITS2 rRNA
Representative chains: L2
Length: 1167 nucleotides
Theoretical weight: 376.43 KDa
111671002003004005006007008009001,0001,100
 
5001000
Chains
Chain C (auth L2)
Interaction interfaces

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Name: 28S ribosomal RNA
Representative chains: L3
Length: 5070 nucleotides
Theoretical weight: 1640.22 KDa
Rfam: Eukaryotic large subunit ribosomal RNA
150705001,0001,5002,0002,5003,0003,5004,0004,5005,000
 
20004000
Chains
Chain D (auth L3)
Rfam
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