6g51

Electron Microscopy
4.1Å resolution

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

Released:
Source organism: Homo sapiens
Related structures: EMD-4350

Function and Biology Details

Reactions catalysed:
ATP + a protein = ADP + a phosphoprotein
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 38-mer (preferred)
Entry contents:
37 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (38 distinct):
40S ribosomal protein S17 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
40S ribosomal protein SA 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:
40S ribosomal protein S3a 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
40S ribosomal protein S2 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:
40S ribosomal protein S4, 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:
40S ribosomal protein S6 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
40S ribosomal protein S7 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
40S ribosomal protein S8 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
40S ribosomal protein S9 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:
40S ribosomal protein S11 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:
40S ribosomal protein S13 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:
40S ribosomal protein S14 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
40S ribosomal protein S21 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
40S ribosomal protein S15a 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
40S ribosomal protein S23 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
40S ribosomal protein S24 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
40S ribosomal protein S27 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
40S ribosomal protein S30 Chain: e
Molecule details ›
Chain: e
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62861 (Residues: 1-59; Coverage: 100%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
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
RNA-binding protein NOB1 Chain: y
Molecule details ›
Chain: y
Length: 412 amino acids
Theoretical weight: 46.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9ULX3 (Residues: 1-412; Coverage: 100%)
Gene names: ART4, MSTP158, NOB1, NOB1P, PSMD8BP1
Sequence domains:
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:
Serine/threonine-protein kinase RIO2 Chain: v
Molecule details ›
Chain: v
Length: 552 amino acids
Theoretical weight: 63.37 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BVS4 (Residues: 1-552; Coverage: 100%)
Gene names: RIO2, RIOK2
Sequence domains:
Protein LTV1 homolog Chain: t
Molecule details ›
Chain: t
Length: 475 amino acids
Theoretical weight: 54.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96GA3 (Residues: 1-475; Coverage: 100%)
Gene names: C6orf93, LTV1
Sequence domains: Low temperature viability protein
40S ribosomal protein S29 Chain: d
Molecule details ›
Chain: d
Length: 56 amino acids
Theoretical weight: 6.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62273 (Residues: 1-56; Coverage: 100%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
40S ribosomal protein S3 Chain: D
Molecule details ›
Chain: D
Length: 243 amino acids
Theoretical weight: 26.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P23396 (Residues: 1-243; Coverage: 100%)
Gene names: OK/SW-cl.26, RPS3
Sequence domains:
40S ribosomal protein S5 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
40S ribosomal protein S10 Chain: K
Molecule details ›
Chain: K
Length: 165 amino acids
Theoretical weight: 18.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46783 (Residues: 1-165; Coverage: 100%)
Gene name: RPS10
Sequence domains: Plectin/S10 domain
40S ribosomal protein S12 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
40S ribosomal protein S15 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
40S ribosomal protein S16 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
40S ribosomal protein S18 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
40S ribosomal protein S19 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
40S ribosomal protein S20 Chain: U
Molecule details ›
Chain: U
Length: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60866 (Residues: 1-119; Coverage: 100%)
Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e
40S ribosomal protein S25 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
40S ribosomal protein S28 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
Ubiquitin-40S ribosomal protein S27a 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:
Receptor of activated protein C kinase 1 Chain: g
Molecule details ›
Chain: g
Length: 317 amino acids
Theoretical weight: 35.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63244 (Residues: 1-317; Coverage: 100%)
Gene names: GNB2L1, HLC7, PIG21, RACK1
Sequence domains: WD domain, G-beta repeat
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1882 nucleotides
Theoretical weight: 607.06 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-4350