Structure analysis

Mus musculus brain neocortex ribosome 60S bound to Ebp1

Electron Microscopy
3.1Å resolution
Source organism: Mus musculus
Assembly composition:
hetero 46-mer (preferred)
Entry contents: 43 distinct polypeptide molecules
3 distinct RNA molecules

Assemblies

Assembly 1 (preferred)
Download    3D Visualisation
Multimeric state: hetero 46-mer
Accessible surface area: 711818.68 Å2
Buried surface area: 408262.9 Å2
Dissociation area: 249.86 Å2
Dissociation energy (ΔGdiss): -4.85 kcal/mol
Dissociation entropy (TΔSdiss): 9.85 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-126720

Macromolecules

PDBe-KB: UniProt Coverage View: P62918  
125220406080100120140160180200220240
 
100200
UniProt
P62918
Chains
Domains
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Ligand binding sites
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Sequence conservation

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PDBe-KB: UniProt Coverage View: P27659  
139450100150200250300350
 
100200300
UniProt
P27659
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Sequence conservation

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PDBe-KB: UniProt Coverage View: Q9D8E6  
136350100150200250300350
 
100200300
UniProt
Q9D8E6
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Chain: D
Length: 294 amino acids
Theoretical weight: 34.13 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P47962 (Residues: 4-297; Coverage: 99%)
Gene name: Rpl5
Pfam:
InterPro:
PDBe-KB: UniProt Coverage View: P47962  
129420406080100120140160180200220240260280
 
100200
UniProt
P47962
Chains
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Chain: E
Length: 194 amino acids
Theoretical weight: 22.36 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P47911 (Residues: 103-296; Coverage: 66%)
Gene name: Rpl6
Pfam: Ribosomal protein L6e
InterPro:
PDBe-KB: UniProt Coverage View: P47911  
119420406080100120140160180
 
50100150
UniProt
P47911
Chains
Domains
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Sequence conservation

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PDBe-KB: UniProt Coverage View: P14148  
123420406080100120140160180200220
 
100200
UniProt
P14148
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PDBe-KB: UniProt Coverage View: P12970  
123420406080100120140160180200220
 
100200
UniProt
P12970
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PDBe-KB: UniProt Coverage View: P51410  
119120406080100120140160180
 
50100150
UniProt
P51410
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PDBe-KB: UniProt Coverage View: Q6ZWV3  
121120406080100120140160180200
 
50100150200
UniProt
Q6ZWV3
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PDBe-KB: UniProt Coverage View: Q9CXW4  
116920406080100120140160
 
50100150
UniProt
Q9CXW4
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Chain: K
Length: 205 amino acids
Theoretical weight: 23.62 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P47963 (Residues: 2-206; Coverage: 97%)
Gene name: Rpl13
Pfam: Ribosomal protein L13e
InterPro:
PDBe-KB: UniProt Coverage View: P47963  
120520406080100120140160180200
 
50100150200
UniProt
P47963
Chains
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PDBe-KB: UniProt Coverage View: Q9CR57  
1139102030405060708090100110120130
 
50100
UniProt
Q9CR57
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Chain: M
Length: 203 amino acids
Theoretical weight: 24.08 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CZM2 (Residues: 2-204; Coverage: 100%)
Gene name: Rpl15
Pfam: Ribosomal L15
InterPro:
PDBe-KB: UniProt Coverage View: Q9CZM2  
120320406080100120140160180200
 
50100150200
UniProt
Q9CZM2
Chains
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PDBe-KB: UniProt Coverage View: P19253  
119520406080100120140160180
 
50100150
UniProt
P19253
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Chain: O
Length: 153 amino acids
Theoretical weight: 17.76 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CPR4 (Residues: 2-154; Coverage: 83%)
Gene name: Rpl17
Pfam: Ribosomal protein L22p/L17e
InterPro:
PDBe-KB: UniProt Coverage View: Q9CPR4  
115320406080100120140
 
50100150
UniProt
Q9CPR4
Chains
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Chain: P
Length: 185 amino acids
Theoretical weight: 21.41 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P35980 (Residues: 4-188; Coverage: 98%)
Gene name: Rpl18
Pfam: Ribosomal protein 60S L18 and 50S L18e
InterPro:
PDBe-KB: UniProt Coverage View: P35980  
118520406080100120140160180
 
50100150
UniProt
P35980
Chains
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Chain: Q
Length: 175 amino acids
Theoretical weight: 20.63 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P62717 (Residues: 1-175; Coverage: 99%)
Gene name: Rpl18a
Pfam: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
InterPro:
PDBe-KB: UniProt Coverage View: P62717  
117520406080100120140160
 
50100150
UniProt
P62717
Chains
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Chain: R
Length: 157 amino acids
Theoretical weight: 18.27 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: O09167 (Residues: 2-158; Coverage: 98%)
Gene name: Rpl21
Pfam: Ribosomal protein L21e
InterPro:
PDBe-KB: UniProt Coverage View: O09167  
115720406080100120140
 
50100150
UniProt
O09167
Chains
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Chain: S
Length: 101 amino acids
Theoretical weight: 11.74 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P67984 (Residues: 16-116; Coverage: 79%)
Gene name: Rpl22
Pfam: Ribosomal L22e protein family
InterPro:
PDBe-KB: UniProt Coverage View: P67984  
1101102030405060708090100
 
50100
UniProt
P67984
Chains
Domains
Sequence conservation

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Chain: T
Length: 129 amino acids
Theoretical weight: 13.83 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P62830 (Residues: 12-140; Coverage: 92%)
Gene name: Rpl23
Pfam: Ribosomal protein L14p/L23e
InterPro:
PDBe-KB: UniProt Coverage View: P62830  
1129102030405060708090100110120
 
50100
UniProt
P62830
Chains
Domains
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Chain: U
Length: 62 amino acids
Theoretical weight: 7.38 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q8BP67 (Residues: 2-63; Coverage: 40%)
Gene name: Rpl24
Pfam: Ribosomal protein L24e
InterPro:
PDBe-KB: UniProt Coverage View: Q8BP67  
16251015202530354045505560
 
204060KVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQ
UniProt
Q8BP67
Chains
Domains
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Sequence conservation

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PDBe-KB: UniProt Coverage View: P62751  
1118102030405060708090100110
 
50100
UniProt
P62751
Chains
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Sequence conservation

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PDBe-KB: UniProt Coverage View: Q4FZH2  
1127102030405060708090100110120
 
50100
UniProt
Q4FZH2
Chains
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Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: Q5BLJ9  
1134102030405060708090100110120130
 
50100
UniProt
Q5BLJ9
Chains
Domains
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: P14115  
114720406080100120140
 
50100
UniProt
P14115
Chains
Domains
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Chain: Z
Length: 68 amino acids
Theoretical weight: 7.96 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P47915 (Residues: 2-69; Coverage: 43%)
Gene names: Rpl29, Rpl43
Pfam: Ribosomal L29e protein family
InterPro: Large ribosomal subunit protein eL29
PDBe-KB: UniProt Coverage View: P47915  
1685101520253035404550556065
 
204060AKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNKKGLKKMQANNAKAVSARA
UniProt
P47915
Chains
Domains
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Chain: a
Length: 97 amino acids
Theoretical weight: 10.81 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P62889 (Residues: 13-109; Coverage: 84%)
Gene name: Rpl30
Pfam: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
InterPro:
PDBe-KB: UniProt Coverage View: P62889  
197102030405060708090
 
50
UniProt
P62889
Chains
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Chain: b
Length: 106 amino acids
Theoretical weight: 12.51 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P62900 (Residues: 18-123; Coverage: 85%)
Gene name: Rpl31
Pfam: Ribosomal protein L31e
InterPro:
PDBe-KB: UniProt Coverage View: P62900  
1106102030405060708090100
 
50100
UniProt
P62900
Chains
Domains
Sequence conservation

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Chain: c
Length: 129 amino acids
Theoretical weight: 15.18 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P62911 (Residues: 2-130; Coverage: 96%)
Gene name: Rpl32
Pfam: Ribosomal protein L32
InterPro:
PDBe-KB: UniProt Coverage View: P62911  
1129102030405060708090100110120
 
50100
UniProt
P62911
Chains
Domains
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chain: d
Length: 109 amino acids
Theoretical weight: 12.45 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: O55142 (Residues: 2-110; Coverage: 99%)
Gene name: Rpl35a
Pfam: Ribosomal protein L35Ae
InterPro:
PDBe-KB: UniProt Coverage View: O55142  
1109102030405060708090100
 
50100
UniProt
O55142
Chains
Domains
Interaction interfaces
Sequence conservation

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Chain: e
Length: 114 amino acids
Theoretical weight: 12.99 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D1R9 (Residues: 2-115; Coverage: 97%)
Gene name: Rpl34
Pfam: Ribosomal protein L34e
InterPro:
PDBe-KB: UniProt Coverage View: Q9D1R9  
1114102030405060708090100110
 
50100
UniProt
Q9D1R9
Chains
Domains
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Chain: f
Length: 122 amino acids
Theoretical weight: 14.46 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q6ZWV7 (Residues: 2-123; Coverage: 99%)
Gene name: Rpl35
Pfam: Ribosomal L29 protein
InterPro:
PDBe-KB: UniProt Coverage View: Q6ZWV7  
1122102030405060708090100110120
 
50100
UniProt
Q6ZWV7
Chains
Domains
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Chain: g
Length: 98 amino acids
Theoretical weight: 11.49 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P47964 (Residues: 4-101; Coverage: 93%)
Gene name: Rpl36
Pfam: Ribosomal protein L36e
InterPro:
PDBe-KB: UniProt Coverage View: P47964  
198102030405060708090
 
50
UniProt
P47964
Chains
Domains
Interaction interfaces
Sequence conservation

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Chain: h
Length: 84 amino acids
Theoretical weight: 9.86 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D823 (Residues: 2-85; Coverage: 87%)
Gene name: Rpl37
Pfam: Ribosomal protein L37e
InterPro:
PDBe-KB: UniProt Coverage View: Q9D823  
1841020304050607080
 
20406080TKGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTGTGRMRHLKIVYRRFRHGFREGTTPK
UniProt
Q9D823
Chains
Domains
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chain: i
Length: 69 amino acids
Theoretical weight: 8.09 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9JJI8 (Residues: 2-70; Coverage: 99%)
Gene name: Rpl38
Pfam: Ribosomal L38e protein family
InterPro:
PDBe-KB: UniProt Coverage View: Q9JJI8  
1695101520253035404550556065
 
204060PRKIEEIKDFLLTARRKDAKSVKIKKNKDNVKFKVRCSRYLYTLVITDKEKAEKLKQSLPPGLAVKDLK
UniProt
Q9JJI8
Chains
Domains
Sequence conservation

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Chain: j
Length: 50 amino acids
Theoretical weight: 6.3 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q505A8 (Residues: 2-51; Coverage: 98%)
Gene name: Rpl39
Pfam: Ribosomal L39 protein
InterPro:
PDBe-KB: UniProt Coverage View: Q505A8  
1505101520253035404550
 
2040SSHKTFRIKRFLAKKQKQNRPIPQWIRMKTGNKIRYNSKRRHWRRTKLGL
UniProt
Q505A8
Chains
Domains
Interaction interfaces
Sequence conservation

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Chain: k
Length: 50 amino acids
Theoretical weight: 5.96 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q5M9K3 (Residues: 78-127; Coverage: 39%)
Gene name: Uba52
Pfam: Ribosomal L40e family
InterPro:
PDBe-KB: UniProt Coverage View: Q5M9K3  
1505101520253035404550
 
2040IEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKKV
UniProt
Q5M9K3
Chains
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Chain: l
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P62947 (Residues: 1-25; Coverage: 100%)
Gene name: Rpl41
Pfam: Ribosomal protein L41
InterPro: Large ribosomal subunit protein eS32
PDBe-KB: UniProt Coverage View: P62947  
12524681012141618202224
 
1020MRAKWRKKRMRRLKRKRRKMRQRSK
UniProt
P62947
Chains
Domains
Flexibility predictions
Ligand binding sites
Sequence conservation

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Chain: m
Length: 105 amino acids
Theoretical weight: 12.35 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q5M9P1 (Residues: 2-106; Coverage: 99%)
Gene name: Rpl36a
Pfam: Ribosomal protein L44
InterPro:
PDBe-KB: UniProt Coverage View: Q5M9P1  
1105102030405060708090100
 
50100
UniProt
Q5M9P1
Chains
Domains
Flexibility predictions
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Chain: n
Length: 91 amino acids
Theoretical weight: 10.17 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q4VAF2 (Residues: 2-92; Coverage: 99%)
Gene name: Rpl37a
Pfam: Ribosomal L37ae protein family
InterPro:
PDBe-KB: UniProt Coverage View: Q4VAF2  
191102030405060708090
 
20406080
UniProt
Q4VAF2
Chains
Domains
Ligand binding sites
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: P84099  
118420406080100120140160180
 
50100150
UniProt
P84099
Chains
Domains
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Sequence conservation

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Chain: p
Length: 122 amino acids
Theoretical weight: 14.01 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P41105 (Residues: 2-123; Coverage: 89%)
Gene name: Rpl28
Pfam: Ribosomal L28e protein family
InterPro:
PDBe-KB: UniProt Coverage View: P41105  
1122102030405060708090100110120
 
50100
UniProt
P41105
Chains
Domains
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: P50580  
135350100150200250300350
 
100200300
UniProt
P50580
Chains
Domains
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Sequence conservation

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Name: 28S ribosomal RNA
Representative chains: q
Length: 3612 nucleotides
Theoretical weight: 1170.2 KDa
Rfam: Eukaryotic large subunit ribosomal RNA
136125001,0001,5002,0002,5003,0003,500
 
100020003000
Chains
Chain QA (auth q)
Rfam
Ligand binding sites
Interaction interfaces

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Name: 5.8S ribosomal RNA
Representative chains: r
Length: 157 nucleotides
Theoretical weight: 50.45 KDa
Rfam: 5.8S ribosomal RNA
115720406080100120140
 
50100150
Chains
Chain RA (auth r)
Rfam
Ligand binding sites
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Name: 5S ribosomal RNA
Representative chains: s
Length: 119 nucleotides
Theoretical weight: 38.39 KDa
Rfam: 5S ribosomal RNA
1119102030405060708090100110
 
50100
Chains
Chain SA (auth s)
Rfam
Ligand binding sites
Interaction interfaces

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