› › Structure analysis

Cryo-EM structure of a late human pre-40S ribosomal subunit - State A

Electron Microscopy
4.5Å resolution
PDB entry 6g4w coloured by chain, front view.
PDB entry 6g4w coloured by chain, side view.
PDB entry 6g4w coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero 31-mer (preferred)
Entry contents: 30 distinct polypeptide molecules
1 distinct RNA molecule

Quick links

Assemblies

Assembly 1 (preferred)
Download    3D Visualisation
Assembly Name: BUD23-TRM112 methyltransferase complex and RNA
hide full assembly name
Multimeric state: hetero 31-mer
Accessible surface area: 46305.21 Å2
Buried surface area: 0.0 Å2
Dissociation area: 0 Å2
Dissociation energy (ΔGdiss): 0 kcal/mol
Dissociation entropy (TΔSdiss): 0 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-129073

Macromolecules

Small ribosomal subunit protein eS17
Chain: R
Length: 135 amino acids
Theoretical weight: 15.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08708 (Residues: 1-135; Coverage: 100%)
Gene names: RPS17, RPS17L
Pfam: Ribosomal S17
InterPro:
Small ribosomal subunit protein eS17 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS17 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS17 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P08708  
1135102030405060708090100110120130
 
50100
UniProt
P08708
Chains
Domains
Secondary structure
Flexibility predictions
Molecule details ›

Search similar proteins

Small ribosomal subunit protein eS27
Chain: b
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P42677 (Residues: 1-84; Coverage: 100%)
Gene names: MPS1, RPS27
Pfam: Ribosomal protein S27
InterPro:
Small ribosomal subunit protein eS27 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS27 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS27 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P42677  
1841020304050607080
 
20406080MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCSTVLCQPTGGKARLTEGCSFRRKQH
UniProt
P42677
Chains
Domains
Secondary structure
Flexibility predictions
Molecule details ›

Search similar proteins

Small ribosomal subunit protein eS1
Chain: B
Length: 264 amino acids
Theoretical weight: 30 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61247 (Residues: 1-264; Coverage: 100%)
Gene names: FTE1, MFTL, RPS3A
Pfam: Ribosomal S3Ae family
InterPro:
Small ribosomal subunit protein eS1 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS1 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS1 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P61247  
126420406080100120140160180200220240260
 
100200
UniProt
P61247
Chains
Domains
Secondary structure
Flexibility predictions
Molecule details ›

Search similar proteins

Small ribosomal subunit protein eS28
Chain: c
Length: 69 amino acids
Theoretical weight: 7.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62857 (Residues: 1-69; Coverage: 100%)
Gene name: RPS28
Pfam: Ribosomal protein S28e
InterPro:
Small ribosomal subunit protein eS28 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS28 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS28 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62857  
1695101520253035404550556065
 
204060MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR
UniProt
P62857
Chains
Domains
Secondary structure
Flexibility predictions
Molecule details ›

Search similar proteins

Small ribosomal subunit protein eS4, X isoform
Chain: E
Length: 263 amino acids
Theoretical weight: 29.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62701 (Residues: 1-263; Coverage: 100%)
Gene names: CCG2, RPS4, RPS4X, SCAR
Pfam:
InterPro:
Small ribosomal subunit protein eS4, X isoform in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS4, X isoform in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS4, X isoform in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62701  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein eS30
Chain: e
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62861 (Residues: 75-133; Coverage: 44%)
Gene name: FAU
Pfam: Ribosomal protein S30
InterPro: Small ribosomal subunit protein eS30
Small ribosomal subunit protein eS30 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS30 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS30 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62861  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein uS7
Chain: F
Length: 204 amino acids
Theoretical weight: 22.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46782 (Residues: 1-204; Coverage: 100%)
Gene name: RPS5
Pfam: Ribosomal protein S7p/S5e
InterPro:
Small ribosomal subunit protein uS7 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein uS7 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein uS7 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P46782  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein eS7
Chain: H
Length: 194 amino acids
Theoretical weight: 22.17 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62081 (Residues: 1-194; Coverage: 100%)
Gene name: RPS7
Pfam: Ribosomal protein S7e
InterPro:
Small ribosomal subunit protein eS7 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS7 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS7 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62081  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein eS6
Chain: G
Length: 249 amino acids
Theoretical weight: 28.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62753 (Residues: 1-249; Coverage: 100%)
Gene names: OK/SW-cl.2, RPS6
Pfam: Ribosomal protein S6e
InterPro:
Small ribosomal subunit protein eS6 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS6 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS6 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62753  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein eS25
Chain: Z
Length: 125 amino acids
Theoretical weight: 13.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62851 (Residues: 1-125; Coverage: 100%)
Gene name: RPS25
Pfam: S25 ribosomal protein
InterPro:
Small ribosomal subunit protein eS25 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS25 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS25 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62851  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein eS24
Chain: Y
Length: 133 amino acids
Theoretical weight: 15.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62847 (Residues: 1-133; Coverage: 100%)
Gene name: RPS24
Pfam: Ribosomal protein S24e
InterPro:
Small ribosomal subunit protein eS24 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS24 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS24 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62847  
Loading Protvista...
Molecule details ›

Search similar proteins

RNA-binding protein PNO1
Chain: x
Length: 252 amino acids
Theoretical weight: 27.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NRX1 (Residues: 1-252; Coverage: 100%)
Gene name: PNO1
Pfam: Eukaryotic type KH-domain (KH-domain type I) (327.11.2)
InterPro:
RNA-binding protein PNO1 in PDB entry 6g4w, assembly 1, front view.
RNA-binding protein PNO1 in PDB entry 6g4w, assembly 1, side view.
RNA-binding protein PNO1 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q9NRX1  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein uS12
Chain: X
Length: 143 amino acids
Theoretical weight: 15.84 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62266 (Residues: 1-143; Coverage: 100%)
Gene name: RPS23
Pfam: Ribosomal protein S12/S23
InterPro:
Small ribosomal subunit protein uS12 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein uS12 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein uS12 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62266  
Loading Protvista...
Molecule details ›

Search similar proteins

Bystin
Chain: w
Length: 437 amino acids
Theoretical weight: 49.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13895 (Residues: 1-437; Coverage: 100%)
Gene names: BYSL, ENP1
Pfam: Bystin
InterPro: Bystin
Bystin in PDB entry 6g4w, assembly 1, front view.
Bystin in PDB entry 6g4w, assembly 1, side view.
Bystin in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q13895  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein uS8
Chain: W
Length: 130 amino acids
Theoretical weight: 14.87 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62244 (Residues: 1-130; Coverage: 100%)
Gene names: OK/SW-cl.82, RPS15A
Pfam: Ribosomal protein S8
InterPro:
Small ribosomal subunit protein uS8 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein uS8 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein uS8 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62244  
Loading Protvista...
Molecule details ›

Search similar proteins

Pre-rRNA-processing protein TSR1 homolog
Chain: u
Length: 804 amino acids
Theoretical weight: 91.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q2NL82 (Residues: 1-804; Coverage: 100%)
Gene names: KIAA1401, TSR1
Pfam:
InterPro:
Pre-rRNA-processing protein TSR1 homolog in PDB entry 6g4w, assembly 1, front view.
Pre-rRNA-processing protein TSR1 homolog in PDB entry 6g4w, assembly 1, side view.
Pre-rRNA-processing protein TSR1 homolog in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q2NL82  
Loading Protvista...
Molecule details ›

Search similar proteins

Protein LTV1 homolog
Chain: t
Length: 18 amino acids
Theoretical weight: 2.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96GA3 (Residues: 352-369; Coverage: 4%)
Gene names: C6orf93, LTV1
Protein LTV1 homolog in PDB entry 6g4w, assembly 1, front view.
Protein LTV1 homolog in PDB entry 6g4w, assembly 1, side view.
Protein LTV1 homolog in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q96GA3  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein eS19
Chain: T
Length: 145 amino acids
Theoretical weight: 16.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39019 (Residues: 1-145; Coverage: 100%)
Gene name: RPS19
Pfam: Ribosomal protein S19e
InterPro:
Small ribosomal subunit protein eS19 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS19 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS19 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P39019  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein uS13
Chain: S
Length: 152 amino acids
Theoretical weight: 17.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62269 (Residues: 1-152; Coverage: 100%)
Gene names: D6S218E, RPS18
Pfam: Ribosomal protein S13/S18
InterPro:
Small ribosomal subunit protein uS13 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein uS13 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein uS13 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62269  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein uS9
Chain: Q
Length: 146 amino acids
Theoretical weight: 16.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62249 (Residues: 1-146; Coverage: 100%)
Gene name: RPS16
Pfam: Ribosomal protein S9/S16
InterPro:
Small ribosomal subunit protein uS9 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein uS9 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein uS9 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62249  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein uS19
Chain: P
Length: 145 amino acids
Theoretical weight: 17.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62841 (Residues: 1-145; Coverage: 100%)
Gene names: RIG, RPS15
Pfam: Ribosomal protein S19
InterPro:
Small ribosomal subunit protein uS19 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein uS19 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein uS19 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62841  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein uS11
Chain: O
Length: 151 amino acids
Theoretical weight: 16.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62263 (Residues: 1-151; Coverage: 100%)
Gene names: PRO2640, RPS14
Pfam: Ribosomal protein S11
InterPro:
Small ribosomal subunit protein uS11 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein uS11 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein uS11 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62263  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein uS15
Chain: N
Length: 151 amino acids
Theoretical weight: 17.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62277 (Residues: 1-151; Coverage: 100%)
Gene name: RPS13
Pfam:
InterPro:
Small ribosomal subunit protein uS15 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein uS15 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein uS15 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62277  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein uS17
Chain: L
Length: 158 amino acids
Theoretical weight: 18.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62280 (Residues: 1-158; Coverage: 100%)
Gene name: RPS11
Pfam:
InterPro:
Small ribosomal subunit protein uS17 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein uS17 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein uS17 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62280  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein uS4
Chain: J
Length: 194 amino acids
Theoretical weight: 22.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46781 (Residues: 1-194; Coverage: 100%)
Gene name: RPS9
Pfam:
InterPro:
Small ribosomal subunit protein uS4 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein uS4 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein uS4 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P46781  
Loading Protvista...
Molecule details ›

Search similar proteins

Small ribosomal subunit protein eS8
Chain: I
Length: 208 amino acids
Theoretical weight: 24.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62241 (Residues: 1-208; Coverage: 100%)
Gene names: OK/SW-cl.83, RPS8
Pfam: Ribosomal protein S8e
InterPro:
Small ribosomal subunit protein eS8 in PDB entry 6g4w, assembly 1, front view.
Small ribosomal subunit protein eS8 in PDB entry 6g4w, assembly 1, side view.
Small ribosomal subunit protein eS8 in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P62241  
Loading Protvista...
Molecule details ›

Search similar proteins

RRP12
Chain: s
Length: 800 amino acids
Theoretical weight: 68.1 KDa
Source organism: Homo sapiens
RRP12 in PDB entry 6g4w, assembly 1, front view.
RRP12 in PDB entry 6g4w, assembly 1, side view.
RRP12 in PDB entry 6g4w, assembly 1, top view.
Loading Protvista...
Molecule details ›

Search similar proteins

Multifunctional methyltransferase subunit TRM112-like protein
Chain: r
Length: 125 amino acids
Theoretical weight: 14.22 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UI30 (Residues: 1-125; Coverage: 100%)
Gene names: AD-001, HSPC152, HSPC170, TRMT112
Pfam: Trm112p-like protein
InterPro:
Multifunctional methyltransferase subunit TRM112-like protein in PDB entry 6g4w, assembly 1, front view.
Multifunctional methyltransferase subunit TRM112-like protein in PDB entry 6g4w, assembly 1, side view.
Multifunctional methyltransferase subunit TRM112-like protein in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q9UI30  
Loading Protvista...
Molecule details ›

Search similar proteins

18S rRNA (guanine-N(7))-methyltransferase
Chain: q
Length: 281 amino acids
Theoretical weight: 31.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43709 (Residues: 1-281; Coverage: 100%)
Gene names: BUD23, HUSSY-03, MERM1, PP3381, WBSCR22
Pfam:
InterPro:
Probable 18S rRNA (guanine-N(7))-methyltransferase in PDB entry 6g4w, assembly 1, front view.
Probable 18S rRNA (guanine-N(7))-methyltransferase in PDB entry 6g4w, assembly 1, side view.
Probable 18S rRNA (guanine-N(7))-methyltransferase in PDB entry 6g4w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: O43709  
Loading Protvista...
Molecule details ›

Search similar proteins

UNKNOWN HELIX
Chain: k
Length: 19 amino acids
Theoretical weight: 1.37 KDa
Source organism: Homo sapiens
UNKNOWN HELIX in PDB entry 6g4w, assembly 1, front view.
UNKNOWN HELIX in PDB entry 6g4w, assembly 1, side view.
UNKNOWN HELIX in PDB entry 6g4w, assembly 1, top view.
Loading Protvista...
Molecule details ›

Search similar proteins

RNA chain 2
Name: 18S Ribosomal RNA
Representative chains: 2
Length: 1882 nucleotides
Theoretical weight: 607.06 KDa
18S Ribosomal RNA in PDB entry 6g4w, assembly 1, front view.
18S Ribosomal RNA in PDB entry 6g4w, assembly 1, side view.
18S Ribosomal RNA in PDB entry 6g4w, assembly 1, top view.
Loading Protvista...
Molecule details ›

Search similar RNA

Quick links