Structure analysis

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model

Electron Microscopy
3.04Å resolution
Assembly composition:
hetero 26-mer (preferred)
Entry contents: 24 distinct polypeptide molecules
2 distinct RNA molecules

Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 26-mer
Accessible surface area: 263528.67 Å2
Buried surface area: 101229.63 Å2
Dissociation area: 442.21 Å2
Dissociation energy (ΔGdiss): -1.59 kcal/mol
Dissociation entropy (TΔSdiss): 9.28 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-220475

Macromolecules

Chain: 5
Length: 235 amino acids
Theoretical weight: 28.03 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q04031 (Residues: 1-235; Coverage: 100%)
Gene names: RRP17, YDR412W
Pfam: Nucleolar protein 12 (25kDa)
InterPro: Nucleolar protein 12
PDBe-KB: UniProt Coverage View: Q04031  
123520406080100120140160180200220
 
100200
UniProt
Q04031
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Domains
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Chain: 8
Length: 710 amino acids
Theoretical weight: 81.72 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P39744 (Residues: 1-710; Coverage: 100%)
Gene names: NOC2, YOR206W, YOX001
Pfam: Noc2p family
InterPro: Nucleolar complex protein 2
PDBe-KB: UniProt Coverage View: P39744  
1710100200300400500600700
 
200400600
UniProt
P39744
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PDBe-KB: UniProt Coverage View: P14126  
138750100150200250300350
 
100200300
UniProt
P14126
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PDBe-KB: UniProt Coverage View: P17076  
125620406080100120140160180200220240
 
100200
UniProt
P17076
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Chain: I
Length: 663 amino acids
Theoretical weight: 75.69 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q07896 (Residues: 1-663; Coverage: 100%)
Gene names: NOC3, YLR002C
Pfam:
InterPro:
PDBe-KB: UniProt Coverage View: Q07896  
166350100150200250300350400450500550600650
 
200400600
UniProt
Q07896
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PDBe-KB: UniProt Coverage View: P05740  
118420406080100120140160180
 
50100150
UniProt
P05740
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Domains
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PDBe-KB: UniProt Coverage View: P0CX82  
118920406080100120140160180
 
50100150
UniProt
P0CX82
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Chain: U
Length: 121 amino acids
Theoretical weight: 13.71 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05749 (Residues: 1-121; Coverage: 100%)
Gene names: L2168, RPL22A, YLR061W
Pfam: Ribosomal L22e protein family
InterPro:
PDBe-KB: UniProt Coverage View: P05749  
1121102030405060708090100110120
 
50100
UniProt
P05749
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Chain: V
Length: 36 amino acids
Theoretical weight: 4.02 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX41 (Residues: 17-74; Coverage: 23%)
Gene names: RPL17A, RPL17AA, RPL23A, YBL0713, YBL087C
Pfam: Ribosomal protein L14p/L23e
PDBe-KB: UniProt Coverage View: P0CX41  
1365101520253035
 
102030LPVGAIMNCARNLYIIMATVKKGKPELRKKVMEDNA
UniProt
P0CX41
Chains
Secondary structure
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PDBe-KB: UniProt Coverage View: P04456  
1142102030405060708090100110120130140
 
50100
UniProt
P04456
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PDBe-KB: UniProt Coverage View: P0C2H6  
1136102030405060708090100110120130
 
50100
UniProt
P0C2H6
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PDBe-KB: UniProt Coverage View: Q02892  
164750100150200250300350400450500550600
 
200400600
UniProt
Q02892
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PDBe-KB: UniProt Coverage View: P14120  
1105102030405060708090100
 
50100
UniProt
P14120
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Chain: d
Length: 113 amino acids
Theoretical weight: 12.98 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0C2H8 (Residues: 1-113; Coverage: 100%)
Gene names: D2478, RPL31A, RPL34, RPL34A, YDL075W
Pfam: Ribosomal protein L31e
InterPro:
PDBe-KB: UniProt Coverage View: P0C2H8  
1113102030405060708090100110
 
50100
UniProt
P0C2H8
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Chain: g
Length: 121 amino acids
Theoretical weight: 13.67 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P87262 (Residues: 1-121; Coverage: 100%)
Gene names: RPL34A, YER056BC, YER056C-A
Pfam: Ribosomal protein L34e
InterPro:
PDBe-KB: UniProt Coverage View: P87262  
1121102030405060708090100110120
 
50100
UniProt
P87262
Chains
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Ligand binding sites
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Chain: k
Length: 78 amino acids
Theoretical weight: 8.85 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P49167 (Residues: 1-78; Coverage: 100%)
Gene names: L8543.2, RPL38, YLR325C
Pfam: Ribosomal L38e protein family
InterPro:
PDBe-KB: UniProt Coverage View: P49167  
17810203040506070
 
204060MAREITDIKQFLELTRRADVKTATVKINKKLNKAGKPFRQTKFKVRGSSSLYTLVINDAGKAKKLIQSLPPTLKVNRL
UniProt
P49167
Chains
Domains
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Chain: m
Length: 429 amino acids
Theoretical weight: 48.69 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q04660 (Residues: 392-563, 564-807; Coverage: 51%)
Gene names: ERB1, YM9796.02C, YMR049C
Pfam: WD domain, G-beta repeat
InterPro:
PDBe-KB: UniProt Coverage View: Q04660  
142950100150200250300350400
 
200400
UniProt
Q04660
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Chain: n
Length: 104 amino acids
Theoretical weight: 12.45 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P53261 (Residues: 1-110; Coverage: 17%)
Gene names: NOP7, RRP13, YGR103W, YPH1
Pfam: Pescadillo N-terminus
InterPro: Pescadillo
PDBe-KB: UniProt Coverage View: P53261  
1104102030405060708090100
 
50100
UniProt
P53261
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PDBe-KB: UniProt Coverage View: Q12024  
146050100150200250300350400450
 
200400
UniProt
Q12024
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PDBe-KB: UniProt Coverage View: P40693  
132250100150200250300
 
100200300
UniProt
P40693
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Domains
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Chain: u
Length: 199 amino acids
Theoretical weight: 24.03 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q07915 (Residues: 1-199; Coverage: 100%)
Gene names: RLP24, YLR009W
Pfam: Ribosomal protein L24e
InterPro:
PDBe-KB: UniProt Coverage View: Q07915  
119920406080100120140160180
 
50100150200
UniProt
Q07915
Chains
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PDBe-KB: UniProt Coverage View: P25582  
1841100200300400500600700800
 
200400600800
UniProt
P25582
Chains
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Chain: j
Length: 88 amino acids
Theoretical weight: 9.88 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P49166 (Residues: 1-88; Coverage: 100%)
Gene names: L9470.6, RPL35A, RPL37A, YLR185W
Pfam: Ribosomal protein L37e
InterPro:
PDBe-KB: UniProt Coverage View: P49166  
1881020304050607080
 
20406080MGKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASKASA
UniProt
P49166
Chains
Domains
Secondary structure
Sequence conservation

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PDBe-KB: UniProt Coverage View: P25808  
160650100150200250300350400450500550600
 
200400600
UniProt
P25808
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Name: 25S ribosomal RNA
Representative chains: 1
Length: 697 nucleotides
Theoretical weight: 225.36 KDa
Rfam: Eukaryotic large subunit ribosomal RNA
169750100150200250300350400450500550600650
 
200400600
Chains
Chain A (auth 1)
Rfam
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Name: 5.8S ribosomal RNA
Representative chains: 2
Length: 72 nucleotides
Theoretical weight: 23.07 KDa
17210203040506070
 
204060GAACGCGCGAUACUCUUUGAACGCACAUUGCGCCCCUUGGUAUUCCAGGGGGCAUCUUUGAAAGCGUAUUGC
Chains
Chain B (auth 2)
Interaction interfaces

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