Structure analysis

Specific features and methylation sites of a plant ribosome. 60S ribosomal subunit.

Electron Microscopy
2.35Å resolution
Source organism: Solanum lycopersicum
Assembly composition:
hetero 45-mer (preferred)
Entry contents: 41 distinct polypeptide molecules
4 distinct RNA molecules

Assemblies

Assembly 1 (preferred)
Download    3D Visualisation
Multimeric state: hetero 45-mer
Accessible surface area: 585147.44 Å2
Buried surface area: 476693.93 Å2
Dissociation area: 1,683.64 Å2
Dissociation energy (ΔGdiss): 12.68 kcal/mol
Dissociation entropy (TΔSdiss): 12.38 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-102780

Macromolecules

PDBe-KB: UniProt Coverage View: P29766  
126020406080100120140160180200220240260
 
100200
UniProt
P29766
Chains
Domains
Flexibility predictions
Ligand binding sites
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: A0A3Q7HW81  
140650100150200250300350400
 
100200300400
UniProt
A0A3Q7HW81
Chains
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PDBe-KB: UniProt Coverage View: Q6SKP4  
138950100150200250300350
 
100200300
UniProt
Q6SKP4
Chains
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PDBe-KB: UniProt Coverage View: A0A3Q7H274  
130120406080100120140160180200220240260280300
 
100200300
UniProt
A0A3Q7H274
Chains
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PDBe-KB: UniProt Coverage View: A0A3Q7GMA5  
122920406080100120140160180200220
 
100200
UniProt
A0A3Q7GMA5
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PDBe-KB: UniProt Coverage View: M1BRF8  
124220406080100120140160180200220240
 
100200
UniProt
M1BRF8
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PDBe-KB: UniProt Coverage View: A0A3Q7GV73  
125820406080100120140160180200220240
 
100200
UniProt
A0A3Q7GV73
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PDBe-KB: UniProt Coverage View: A0A3Q7JDZ0  
119420406080100120140160180
 
50100150
UniProt
A0A3Q7JDZ0
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Domains
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PDBe-KB: UniProt Coverage View: Q3SC85  
122020406080100120140160180200220
 
100200
UniProt
Q3SC85
Chains
Domains
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PDBe-KB: UniProt Coverage View: K4CG62  
118120406080100120140160180
 
50100150
UniProt
K4CG62
Chains
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Chain: N
Length: 206 amino acids
Theoretical weight: 23.62 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7JCM5 (Residues: 1-206; Coverage: 100%)
Gene name: LOC101262297
Pfam: Ribosomal protein L13e
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7JCM5  
120620406080100120140160180200
 
50100150200
UniProt
A0A3Q7JCM5
Chains
Domains
Ligand binding sites
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PDBe-KB: UniProt Coverage View: A0A3Q7J0J5  
1133102030405060708090100110120130
 
50100
UniProt
A0A3Q7J0J5
Chains
Domains
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PDBe-KB: UniProt Coverage View: A0A3Q7HQH0  
120420406080100120140160180200
 
50100150200
UniProt
A0A3Q7HQH0
Chains
Domains
Ligand binding sites
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PDBe-KB: UniProt Coverage View: A0A6N2B4A3  
120620406080100120140160180200
 
50100150200
UniProt
A0A6N2B4A3
Chains
Domains
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PDBe-KB: UniProt Coverage View: A0A3Q7FNQ5  
117320406080100120140160
 
50100150
UniProt
A0A3Q7FNQ5
Chains
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Chain: S
Length: 187 amino acids
Theoretical weight: 20.76 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7I5W4 (Residues: 1-187; Coverage: 100%)
Gene name: LOC101267842
Pfam: Ribosomal protein 60S L18 and 50S L18e
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7I5W4  
118720406080100120140160180
 
50100150
UniProt
A0A3Q7I5W4
Chains
Domains
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PDBe-KB: UniProt Coverage View: A0A3Q7GQ29  
121320406080100120140160180200
 
100200
UniProt
A0A3Q7GQ29
Chains
Domains
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Chain: U
Length: 178 amino acids
Theoretical weight: 21.48 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7IGB1 (Residues: 1-178; Coverage: 100%)
Pfam: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7IGB1  
117820406080100120140160
 
50100150
UniProt
A0A3Q7IGB1
Chains
Domains
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PDBe-KB: UniProt Coverage View: A0A3Q7IJQ0  
116420406080100120140160
 
50100150
UniProt
A0A3Q7IJQ0
Chains
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Chain: W
Length: 124 amino acids
Theoretical weight: 14 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7I7E8 (Residues: 1-124; Coverage: 100%)
Pfam: Ribosomal L22e protein family
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7I7E8  
1124102030405060708090100110120
 
50100
UniProt
A0A3Q7I7E8
Chains
Domains
Sequence conservation

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Chain: X
Length: 140 amino acids
Theoretical weight: 15.04 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: K4CUW3 (Residues: 1-140; Coverage: 100%)
Pfam: Ribosomal protein L14p/L23e
InterPro:
PDBe-KB: UniProt Coverage View: K4CUW3  
1140102030405060708090100110120130140
 
50100
UniProt
K4CUW3
Chains
Domains
Ligand binding sites
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Sequence conservation

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Chain: Y
Length: 165 amino acids
Theoretical weight: 18.71 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7IN69 (Residues: 1-164; Coverage: 100%)
Pfam: Ribosomal protein L24e
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7IN69  
116520406080100120140160
 
50100150
UniProt
A0A3Q7IN69
Chains
Domains
Flexibility predictions
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PDBe-KB: UniProt Coverage View: A0A3Q7INK3  
115420406080100120140
 
50100150
UniProt
A0A3Q7INK3
Chains
Domains
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Sequence conservation

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PDBe-KB: UniProt Coverage View: A0A3Q7FBC6  
114620406080100120140
 
50100
UniProt
A0A3Q7FBC6
Chains
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PDBe-KB: UniProt Coverage View: A0A3Q7GZ83  
1135102030405060708090100110120130
 
50100
UniProt
A0A3Q7GZ83
Chains
Domains
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: A0A0V0H357  
114820406080100120140
 
50100
UniProt
A0A0V0H357
Chains
Domains
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Chain: d
Length: 60 amino acids
Theoretical weight: 6.99 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7GK12 (Residues: 1-60; Coverage: 100%)
Pfam: Ribosomal L29e protein family
InterPro: Large ribosomal subunit protein eL29
PDBe-KB: UniProt Coverage View: A0A3Q7GK12  
16051015202530354045505560
 
204060MAKSKNHTAHNQSYKAHRNGIKKPKSHRHSSTKGMDPKFLRNQRYARKHNKKNGETAAEE
UniProt
A0A3Q7GK12
Chains
Domains
Flexibility predictions
Ligand binding sites
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: A0A3Q7E9D6  
1112102030405060708090100110
 
50100
UniProt
A0A3Q7E9D6
Chains
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Chain: f
Length: 120 amino acids
Theoretical weight: 13.89 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7JRW8 (Residues: 1-120; Coverage: 100%)
Pfam: Ribosomal protein L31e
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7JRW8  
1120102030405060708090100110120
 
50100
UniProt
A0A3Q7JRW8
Chains
Domains
Sequence conservation

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Chain: g
Length: 133 amino acids
Theoretical weight: 15.67 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7F2B5 (Residues: 1-133; Coverage: 100%)
Pfam: Ribosomal protein L32
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7F2B5  
1133102030405060708090100110120130
 
50100
UniProt
A0A3Q7F2B5
Chains
Domains
Ligand binding sites
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: A0A3Q7FPS6  
1112102030405060708090100110
 
50100
UniProt
A0A3Q7FPS6
Chains
Domains
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Chain: i
Length: 120 amino acids
Theoretical weight: 13.82 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7GDM4 (Residues: 1-120; Coverage: 100%)
Pfam: Ribosomal protein L34e
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7GDM4  
1120102030405060708090100110120
 
50100
UniProt
A0A3Q7GDM4
Chains
Domains
Ligand binding sites
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Chain: j
Length: 123 amino acids
Theoretical weight: 14.32 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: Q53U38 (Residues: 1-123; Coverage: 100%)
Pfam: Ribosomal L29 protein
InterPro:
PDBe-KB: UniProt Coverage View: Q53U38  
1123102030405060708090100110120
 
50100
UniProt
Q53U38
Chains
Domains
Interaction interfaces
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Chain: k
Length: 110 amino acids
Theoretical weight: 12.41 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7GUG2 (Residues: 37-146; Coverage: 75%)
Pfam: Ribosomal protein L36e
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7GUG2  
1110102030405060708090100110
 
50100
UniProt
A0A3Q7GUG2
Chains
Domains
Flexibility predictions
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Chain: l
Length: 95 amino acids
Theoretical weight: 10.81 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7FV98 (Residues: 1-95; Coverage: 100%)
Pfam: Ribosomal protein L37e
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7FV98  
195102030405060708090
 
50
UniProt
A0A3Q7FV98
Chains
Domains
Ligand binding sites
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Sequence conservation

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Chain: m
Length: 69 amino acids
Theoretical weight: 8.1 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: P46291 (Residues: 1-69; Coverage: 100%)
Gene name: RPL38
Pfam: Ribosomal L38e protein family
InterPro:
PDBe-KB: UniProt Coverage View: P46291  
1695101520253035404550556065
 
204060MPKQIHEIKDFLLTARRKDARTVKIKKNKDMVKFKVRCSKYLYTLCVSDFEKADKLKQSLPPGLSVQDL
UniProt
P46291
Chains
Domains
Sequence conservation

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Chain: n
Length: 51 amino acids
Theoretical weight: 6.49 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7J415 (Residues: 1-51; Coverage: 100%)
Pfam: Ribosomal L39 protein
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7J415  
1515101520253035404550
 
2040MPSHKSFMIKKKLAKKQRQNRPIPYWIRMRTDNTIRYNAKRRHWRRTKLGF
UniProt
A0A3Q7J415
Chains
Domains
Flexibility predictions
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: K4B017  
1128102030405060708090100110120
 
50100
UniProt
K4B017
Chains
Domains
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chain: p
Length: 105 amino acids
Theoretical weight: 12.04 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7H1I0 (Residues: 1-105; Coverage: 100%)
Pfam: Ribosomal protein L44
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7H1I0  
1105102030405060708090100
 
50100
UniProt
A0A3Q7H1I0
Chains
Domains
Flexibility predictions
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Chain: q
Length: 92 amino acids
Theoretical weight: 10.28 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: K4CND1 (Residues: 1-92; Coverage: 100%)
Pfam: Ribosomal L37ae protein family
InterPro:
PDBe-KB: UniProt Coverage View: K4CND1  
192102030405060708090
 
20406080
UniProt
K4CND1
Chains
Domains
Ligand binding sites
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Chain: r
Length: 143 amino acids
Theoretical weight: 16.02 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7FVJ9 (Residues: 1-143; Coverage: 100%)
Pfam: Ribosomal L28e protein family
InterPro:
PDBe-KB: UniProt Coverage View: A0A3Q7FVJ9  
114320406080100120140
 
50100
UniProt
A0A3Q7FVJ9
Chains
Domains
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Name: tRNA
Representative chains: s
Length: 2 nucleotides
Theoretical weight: 589 Da
121.01.11.21.31.41.51.61.71.81.92.0
 
123CA
Chains
Chain PA (auth s)
Interaction interfaces

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Name: 25S ribosomal RNA
Representative chains: 2
Length: 3391 nucleotides
Theoretical weight: 1098.45 KDa
Rfam: Eukaryotic large subunit ribosomal RNA
133915001,0001,5002,0002,5003,000
 
100020003000
Chains
Chain QA (auth 2)
Rfam
Ligand binding sites
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Name: 5S ribosomal RNA
Representative chains: 5
Length: 120 nucleotides
Theoretical weight: 38.63 KDa
Rfam: 5S ribosomal RNA
1120102030405060708090100110120
 
50100
Chains
Chain RA (auth 5)
Rfam
Ligand binding sites
Interaction interfaces

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Name: 5.8S ribosomal RNA
Representative chains: 8
Length: 165 nucleotides
Theoretical weight: 53.17 KDa
Rfam: 5.8S ribosomal RNA
116520406080100120140160
 
50100150
Chains
Chain SA (auth 8)
Rfam
Ligand binding sites
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