› 7wtv

Electron Microscopy
3.5Å resolution

Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A2

Released:
DOI: 10.2210/pdb7wtv/pdb
PDB entry 7wtv coloured by chain, front view.
PDB entry 7wtv coloured by chain, side view.
PDB entry 7wtv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The nucleoplasmic phase of pre-40S formation prior to nuclear export.
Cheng J, Lau B, Thoms M, Ameismeier M, Berninghausen O, Hurt E, Beckmann R
Nucleic Acids Res (2022)
PMID: 36321656
Related structures: EMD-32802

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 35-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129070 (preferred)
Entry contents:
34 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (35 distinct):
Small ribosomal subunit protein eS17 Chain: R
Molecule details ›
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
Sequence domains: Ribosomal S17
Small ribosomal subunit protein eS27 Chain: b
Molecule details ›
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
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS1 Chain: B
Molecule details ›
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
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein eS28 Chain: c
Molecule details ›
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
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein eS4, X isoform Chain: E
Molecule details ›
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
Sequence domains:
Small ribosomal subunit protein eS30 Chain: e
Molecule details ›
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
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein uS7 Chain: F
Molecule details ›
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
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein eS7 Chain: H
Molecule details ›
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
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS6 Chain: G
Molecule details ›
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
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS25 Chain: Z
Molecule details ›
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
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS24 Chain: Y
Molecule details ›
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
Sequence domains: Ribosomal protein S24e
RNA-binding protein PNO1 Chain: x
Molecule details ›
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
Small ribosomal subunit protein uS12 Chain: X
Molecule details ›
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
Sequence domains: Ribosomal protein S12/S23
Bystin Chain: w
Molecule details ›
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
Sequence domains: Bystin
Small ribosomal subunit protein uS8 Chain: W
Molecule details ›
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
Sequence domains: Ribosomal protein S8
Pre-rRNA-processing protein TSR1 homolog Chain: u
Molecule details ›
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
Sequence domains:
Small ribosomal subunit protein eS19 Chain: T
Molecule details ›
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
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS13 Chain: S
Molecule details ›
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
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS9 Chain: Q
Molecule details ›
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
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS19 Chain: P
Molecule details ›
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
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS11 Chain: O
Molecule details ›
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
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS15 Chain: N
Molecule details ›
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
Sequence domains:
Small ribosomal subunit protein uS17 Chain: L
Molecule details ›
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
Sequence domains:
Small ribosomal subunit protein uS4 Chain: J
Molecule details ›
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
Sequence domains:
Small ribosomal subunit protein eS8 Chain: I
Molecule details ›
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
Sequence domains: Ribosomal protein S8e
Multifunctional methyltransferase subunit TRM112-like protein Chain: r
Molecule details ›
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
Sequence domains: Trm112p-like protein
Probable 18S rRNA (guanine-N(7))-methyltransferase Chain: q
Molecule details ›
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
Sequence domains:
RRP12-like protein Chain: K
Molecule details ›
Chain: K
Length: 1297 amino acids
Theoretical weight: 143.92 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q5JTH9 (Residues: 1-1297; Coverage: 100%)
Gene names: KIAA0690, RRP12
Sequence domains: Ribosomal RNA-processing protein 12, HEAT repeats
Small ribosomal subunit protein eS12 Chain: M
Molecule details ›
Chain: M
Length: 132 amino acids
Theoretical weight: 14.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25398 (Residues: 1-132; Coverage: 100%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Ubiquitin-ribosomal protein eS31 fusion protein Chain: f
Molecule details ›
Chain: f
Length: 156 amino acids
Theoretical weight: 18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62979 (Residues: 1-156; Coverage: 100%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains:
Ribosome biogenesis protein SLX9 homolog Chain: z
Molecule details ›
Chain: z
Length: 230 amino acids
Theoretical weight: 25.5 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NSI2 (Residues: 1-230; Coverage: 100%)
Gene names: C21orf70, FAM207A, PRED56, SLX9
Sequence domains: Ribosome biogenesis protein SLX9
Small ribosomal subunit protein uS2 Chain: A
Molecule details ›
Chain: A
Length: 295 amino acids
Theoretical weight: 32.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08865 (Residues: 1-295; Coverage: 100%)
Gene names: LAMBR, LAMR1, RPSA
Sequence domains:
Small ribosomal subunit protein uS5 Chain: C
Molecule details ›
Chain: C
Length: 293 amino acids
Theoretical weight: 31.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P15880 (Residues: 1-293; Coverage: 100%)
Gene names: RPS2, RPS4
Sequence domains:
Small ribosomal subunit protein eS21 Chain: V
Molecule details ›
Chain: V
Length: 83 amino acids
Theoretical weight: 9.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63220 (Residues: 1-83; Coverage: 100%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1873 nucleotides
Theoretical weight: 604.12 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand SAH 1 x SAH
1 modified residue:
Ligand G7M 1 x G7M

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-32802

Quick links

Citations

2 review citations

Ribosome biogenesis factors-from names to functions.
Dörner et al. (2023)
1 more

1 mention without citation

The nucleoplasmic phase of pre-40S formation prior to nuclear export.
Cheng et al. (2022)