› 7tql

Electron Microscopy
3.2Å resolution

CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B.

Released:
DOI: 10.2210/pdb7tql/pdb
PDB entry 7tql coloured by chain, front view.
PDB entry 7tql coloured by chain, side view.
PDB entry 7tql coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining.
Lapointe CP, Grosely R, Sokabe M, Alvarado C, Wang J, Montabana E, Villa N, Shin BS, Dever TE, Fraser CS, Fernández IS, Puglisi JD
Nature 607 185-190 (2022)
PMID: 35732735
Related structures: EMD-26067

Function and Biology Details

Reactions catalysed: 
GTP + H(2)O = GDP + phosphate
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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 38-mer (preferred)
PDBe Complex ID:
PDB-CPX-130100 (preferred)
Entry contents:
35 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (37 distinct):
Eukaryotic translation initiation factor 5B Chain: 1
Molecule details ›
Chain: 1
Length: 619 amino acids
Theoretical weight: 69.87 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60841 (Residues: 602-625, 626-1219; Coverage: 51%)
Gene names: EIF5B, IF2, KIAA0741
Sequence domains:
Eukaryotic translation initiation factor 1A, X-chromosomal Chain: 4
Molecule details ›
Chain: 4
Length: 90 amino acids
Theoretical weight: 10.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P47813 (Residues: 24-113; Coverage: 63%)
Gene names: EIF1A, EIF1AX, EIF4C
Sequence domains: Translation initiation factor 1A / IF-1
Small ribosomal subunit protein eS1; Small ribosomal subunit protein uS2 Chains: B, C
Molecule details ›
Chains: B, C
Length: 419 amino acids
Theoretical weight: 47.84 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P08865 (Residues: 2-207; Coverage: 70%)
  • Canonical: P61247 (Residues: 21-233; Coverage: 81%)
Gene names: FTE1, LAMBR, LAMR1, MFTL, RPS3A, RPSA
Sequence domains:
Small ribosomal subunit protein uS5 Chain: D
Molecule details ›
Chain: D
Length: 218 amino acids
Theoretical weight: 24.09 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P15880 (Residues: 59-276; Coverage: 74%)
Gene names: RPS2, RPS4
Sequence domains:
Small ribosomal subunit protein eS4, X isoform Chain: E
Molecule details ›
Chain: E
Length: 258 amino acids
Theoretical weight: 29.16 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62701 (Residues: 2-259; Coverage: 98%)
Gene names: CCG2, RPS4, RPS4X, SCAR
Sequence domains:
Small ribosomal subunit protein uS3 Chain: F
Molecule details ›
Chain: F
Length: 225 amino acids
Theoretical weight: 24.97 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P23396 (Residues: 3-227; Coverage: 93%)
Gene names: OK/SW-cl.26, RPS3
Sequence domains:
Small ribosomal subunit protein eS6 Chain: G
Molecule details ›
Chain: G
Length: 226 amino acids
Theoretical weight: 26.16 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62753 (Residues: 1-226; Coverage: 91%)
Gene names: OK/SW-cl.2, RPS6
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7 Chain: H
Molecule details ›
Chain: H
Length: 185 amino acids
Theoretical weight: 21.19 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62081 (Residues: 8-192; Coverage: 95%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8 Chain: I
Molecule details ›
Chain: I
Length: 205 amino acids
Theoretical weight: 23.95 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62241 (Residues: 2-206; Coverage: 99%)
Gene names: OK/SW-cl.83, RPS8
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4 Chain: J
Molecule details ›
Chain: J
Length: 180 amino acids
Theoretical weight: 21.28 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P46781 (Residues: 2-181; Coverage: 93%)
Gene name: RPS9
Sequence domains:
Small ribosomal subunit protein uS7 Chain: K
Molecule details ›
Chain: K
Length: 189 amino acids
Theoretical weight: 21.33 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P46782 (Residues: 16-204; Coverage: 93%)
Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS17 Chain: L
Molecule details ›
Chain: L
Length: 147 amino acids
Theoretical weight: 17.17 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62280 (Residues: 2-148; Coverage: 93%)
Gene name: RPS11
Sequence domains:
Small ribosomal subunit protein eS10 Chain: M
Molecule details ›
Chain: M
Length: 97 amino acids
Theoretical weight: 11.62 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P46783 (Residues: 1-97; Coverage: 59%)
Gene name: RPS10
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein uS15 Chain: N
Molecule details ›
Chain: N
Length: 141 amino acids
Theoretical weight: 16.34 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62277 (Residues: 2-142; Coverage: 93%)
Gene name: RPS13
Sequence domains:
Small ribosomal subunit protein eS12 Chain: O
Molecule details ›
Chain: O
Length: 120 amino acids
Theoretical weight: 13.35 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P25398 (Residues: 10-129; Coverage: 91%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS11 Chain: P
Molecule details ›
Chain: P
Length: 134 amino acids
Theoretical weight: 14.34 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62263 (Residues: 18-151; Coverage: 89%)
Gene names: PRO2640, RPS14
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS19 Chain: Q
Molecule details ›
Chain: Q
Length: 115 amino acids
Theoretical weight: 13.59 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62841 (Residues: 15-129; Coverage: 79%)
Gene names: RIG, RPS15
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS9 Chain: R
Molecule details ›
Chain: R
Length: 139 amino acids
Theoretical weight: 15.77 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62249 (Residues: 8-146; Coverage: 95%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS17 Chain: S
Molecule details ›
Chain: S
Length: 132 amino acids
Theoretical weight: 15.25 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P08708 (Residues: 2-133; Coverage: 98%)
Gene names: RPS17, RPS17L
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS13 Chain: T
Molecule details ›
Chain: T
Length: 140 amino acids
Theoretical weight: 16.5 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62269 (Residues: 3-142; Coverage: 92%)
Gene names: D6S218E, RPS18
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein eS19 Chain: U
Molecule details ›
Chain: U
Length: 139 amino acids
Theoretical weight: 15.41 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P39019 (Residues: 4-142; Coverage: 96%)
Gene name: RPS19
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 Chain: V
Molecule details ›
Chain: V
Length: 101 amino acids
Theoretical weight: 11.51 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P60866 (Residues: 17-117; Coverage: 85%)
Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS8 Chain: W
Molecule details ›
Chain: W
Length: 129 amino acids
Theoretical weight: 14.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62244 (Residues: 2-130; Coverage: 99%)
Gene names: OK/SW-cl.82, RPS15A
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS12 Chain: X
Molecule details ›
Chain: X
Length: 141 amino acids
Theoretical weight: 15.63 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62266 (Residues: 2-142; Coverage: 99%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS24 Chain: Y
Molecule details ›
Chain: Y
Length: 123 amino acids
Theoretical weight: 14.36 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62847 (Residues: 4-126; Coverage: 93%)
Gene name: RPS24
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS21 Chain: Z
Molecule details ›
Chain: Z
Length: 82 amino acids
Theoretical weight: 8.98 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P63220 (Residues: 1-82; Coverage: 99%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein eS25 Chain: a
Molecule details ›
Chain: a
Length: 72 amino acids
Theoretical weight: 8.18 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62851 (Residues: 42-113; Coverage: 58%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS27 Chain: b
Molecule details ›
Chain: b
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P42677 (Residues: 2-83; Coverage: 98%)
Gene names: MPS1, RPS27
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS26 Chain: c
Molecule details ›
Chain: c
Length: 99 amino acids
Theoretical weight: 11.34 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62854 (Residues: 2-100; Coverage: 86%)
Gene name: RPS26
Sequence domains: Ribosomal protein S26e
Small ribosomal subunit protein eS28 Chain: d
Molecule details ›
Chain: d
Length: 58 amino acids
Theoretical weight: 6.45 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62857 (Residues: 8-65; Coverage: 84%)
Gene name: RPS28
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein eS30 Chain: e
Molecule details ›
Chain: e
Length: 51 amino acids
Theoretical weight: 5.64 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62861 (Residues: 81-133; Coverage: 35%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein uS14 Chain: f
Molecule details ›
Chain: f
Length: 54 amino acids
Theoretical weight: 6.5 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62273 (Residues: 3-56; Coverage: 96%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein eS31 Chain: g
Molecule details ›
Chain: g
Length: 65 amino acids
Theoretical weight: 7.62 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62979 (Residues: 85-149; Coverage: 42%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein eS32 Chain: h
Molecule details ›
Chain: h
Length: 19 amino acids
Theoretical weight: 2.68 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62945 (Residues: 1-19; Coverage: 76%)
Gene name: RPL41
Sequence domains: Ribosomal protein L41
Small ribosomal subunit protein RACK1 Chain: j
Molecule details ›
Chain: j
Length: 314 amino acids
Theoretical weight: 34.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P63244 (Residues: 2-315; Coverage: 99%)
Gene names: GNB2L1, HLC7, PIG21, RACK1
Sequence domains: WD domain, G-beta repeat
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1656 nucleotides
Theoretical weight: 534.54 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
Human Met-tRNAiMet Chain: 3
Molecule details ›
Chain: 3
Length: 75 nucleotides
Theoretical weight: 24.23 KDa
Sequence domains: tRNA

Ligands and Environments

3 bound ligands:
Ligand GNP 1 x GNP
Ligand 5GP 1 x 5GP
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-26067
Expression systems:
  • Escherichia coli
  • Homo sapiens

Quick links

Citations

2 review citations

Translational regulation by uORFs and start codon selection stringency.
Dever et al. (2023)
1 more

4 mentions without citation

eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining.
Lapointe et al. (2022)
3 more