› 5it9

Electron Microscopy
3.8Å resolution

Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES.

Released:
DOI: 10.2210/pdb5it9/pdb
PDB entry 5it9 coloured by chain, front view.
PDB entry 5it9 coloured by chain, side view.
PDB entry 5it9 coloured by chain, top view.
Source organism: Kluyveromyces lactis
Primary publication:
Structural characterization of ribosome recruitment and translocation by type IV IRES.
Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernández IS
Elife 5 (2016)
PMID: 27159451
Related structures: EMD-8124

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 35-mer (preferred)
PDBe Complex ID:
PDB-CPX-150925 (preferred)
Entry contents:
33 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (35 distinct):
Small ribosomal subunit protein uS2 Chain: A
Molecule details ›
Chain: A
Length: 206 amino acids
Theoretical weight: 22.88 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CN12 (Residues: 2-207; Coverage: 81%)
Gene names: KLLA0E16171g, RPS0
Sequence domains: Ribosomal protein S2
Structure domains: Glucose-6-phosphate isomerase like protein; domain 1
Small ribosomal subunit protein eS1 Chain: B
Molecule details ›
Chain: B
Length: 214 amino acids
Theoretical weight: 24.49 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CWD0 (Residues: 20-233; Coverage: 84%)
Gene names: KLLA0B05060g, RPS1
Sequence domains: Ribosomal S3Ae family
S5 DRBM domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 217 amino acids
Theoretical weight: 23.16 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CKL3 (Residues: 39-255; Coverage: 84%)
Gene name: KLLA0_F09812g
Sequence domains:
Structure domains:
40S ribosomal protein S3 Chain: D
Molecule details ›
Chain: D
Length: 223 amino acids
Theoretical weight: 24.83 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CRK7 (Residues: 3-225; Coverage: 94%)
Gene name: KLLA0_D08305g
Sequence domains:
Structure domains:
40S ribosomal protein S4 Chain: E
Molecule details ›
Chain: E
Length: 260 amino acids
Theoretical weight: 29.49 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CWJ2 (Residues: 2-261; Coverage: 100%)
Gene name: KLLA0_B03652g
Sequence domains:
Structure domains:
Small ribosomal subunit protein uS7 domain-containing protein Chain: F
Molecule details ›
Chain: F
Length: 206 amino acids
Theoretical weight: 22.91 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CRA3 (Residues: 22-227; Coverage: 91%)
Gene name: KLLA0_D10659g
Sequence domains: Ribosomal protein S7p/S5e
Structure domains: Ribosomal protein S7 domain
Small ribosomal subunit protein eS6 Chain: G
Molecule details ›
Chain: G
Length: 226 amino acids
Theoretical weight: 25.81 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CM04 (Residues: 1-226; Coverage: 96%)
Gene names: KLLA0E24090g, RPS6
Sequence domains: Ribosomal protein S6e
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
40S ribosomal protein S7 Chain: H
Molecule details ›
Chain: H
Length: 184 amino acids
Theoretical weight: 21.03 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CTD6 (Residues: 4-187; Coverage: 97%)
Gene name: KLLA0_C13519g
Sequence domains: Ribosomal protein S7e
40S ribosomal protein S8 Chain: I
Molecule details ›
Chain: I
Length: 200 amino acids
Theoretical weight: 22.51 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CMG3 (Residues: 2-201; Coverage: 100%)
Gene name: KLLA0_E20461g
Sequence domains: Ribosomal protein S8e
Structure domains: Ribosomal protein S8e, subdomain
KLLA0E23673p Chain: J
Molecule details ›
Chain: J
Length: 182 amino acids
Theoretical weight: 20.88 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CM18 (Residues: 2-183; Coverage: 97%)
Gene name: KLLA0_E23673g
Sequence domains:
Plectin/eS10 N-terminal domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 96 amino acids
Theoretical weight: 11.42 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CVZ5 (Residues: 1-96; Coverage: 91%)
Gene name: KLLA0_B08173g
Sequence domains: Plectin/S10 domain
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chain: L
Molecule details ›
Chain: L
Length: 155 amino acids
Theoretical weight: 17.71 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CX80 (Residues: 2-156; Coverage: 99%)
Gene name: KLLA0_A10483g
Sequence domains:
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
40S ribosomal protein S12 Chain: M
Molecule details ›
Chain: M
Length: 122 amino acids
Theoretical weight: 13.12 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CLU4 (Residues: 13-134; Coverage: 91%)
Gene name: KLLA0_F00352g
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Structure domains: 60s Ribosomal Protein L30; Chain: A;
Small ribosomal subunit protein uS15 N-terminal domain-containing protein Chain: N
Molecule details ›
Chain: N
Length: 150 amino acids
Theoretical weight: 16.86 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CJK0 (Residues: 2-151; Coverage: 99%)
Gene name: KLLA0_F18040g
Sequence domains:
Structure domains: S15/NS1, RNA-binding
Small ribosomal subunit protein uS11 Chain: O
Molecule details ›
Chain: O
Length: 127 amino acids
Theoretical weight: 13.46 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: P27069 (Residues: 11-137; Coverage: 93%)
Gene names: CRY1, KLLA0B07623g, RPS14
Sequence domains: Ribosomal protein S11
Structure domains: Ribosomal protein S11
Rps15 Chain: P
Molecule details ›
Chain: P
Length: 123 amino acids
Theoretical weight: 14.06 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CKV4 (Residues: 8-130; Coverage: 87%)
Gene name: KLLA0_F07843g
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS9 Chain: Q
Molecule details ›
Chain: Q
Length: 141 amino acids
Theoretical weight: 15.66 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q875N2 (Residues: 3-143; Coverage: 99%)
Gene names: KLLA0E22077g, RPS16
Sequence domains: Ribosomal protein S9/S16
Structure domains: Ribosomal Protein S5; domain 2
KLLA0B01474p Chain: R
Molecule details ›
Chain: R
Length: 129 amino acids
Theoretical weight: 14.73 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CWU3 (Residues: 2-130; Coverage: 95%)
Gene name: KLLA0_B01474g
Sequence domains: Ribosomal S17
Structure domains: Ribosomal protein S17e-like
KLLA0B01562p Chain: S
Molecule details ›
Chain: S
Length: 145 amino acids
Theoretical weight: 16.95 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CWT9 (Residues: 2-146; Coverage: 99%)
Gene name: KLLA0_B01562g
Sequence domains: Ribosomal protein S13/S18
Structure domains: Helicase, Ruva Protein; domain 3
KLLA0A07194p Chain: T
Molecule details ›
Chain: T
Length: 143 amino acids
Theoretical weight: 15.75 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CXM0 (Residues: 2-144; Coverage: 99%)
Gene name: KLLA0_A07194g
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 domain-containing protein Chain: U
Molecule details ›
Chain: U
Length: 106 amino acids
Theoretical weight: 12.03 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CIM1 (Residues: 12-117; Coverage: 91%)
Gene name: KLLA0_F25542g
Sequence domains: Ribosomal protein S10p/S20e
Structure domains: Ribosomal protein S10 domain
Small ribosomal subunit protein eS21 Chain: V
Molecule details ›
Chain: V
Length: 87 amino acids
Theoretical weight: 9.8 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CXT6 (Residues: 1-87; Coverage: 100%)
Gene names: KLLA0A05700g, RPS21
Sequence domains: Ribosomal protein S21e
Structure domains: Hypothetical Cytosolic Protein; Chain: A;
Small ribosomal subunit protein uS8 Chain: W
Molecule details ›
Chain: W
Length: 129 amino acids
Theoretical weight: 14.51 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CW21 (Residues: 2-130; Coverage: 99%)
Gene names: KLLA0B07601g, RPS22
Sequence domains: Ribosomal protein S8
Structure domains:
RPS23 Chain: X
Molecule details ›
Chain: X
Length: 145 amino acids
Theoretical weight: 16.05 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q875M3 (Residues: 1-145; Coverage: 100%)
Sequence domains: Ribosomal protein S12/S23
40S ribosomal protein S24 Chain: Y
Molecule details ›
Chain: Y
Length: 134 amino acids
Theoretical weight: 15.06 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CU44 (Residues: 2-135; Coverage: 99%)
Gene name: KLLA0_C07755g
Sequence domains: Ribosomal protein S24e
Structure domains: Alpha-Beta Plaits
40S ribosomal protein S25 Chain: Z
Molecule details ›
Chain: Z
Length: 70 amino acids
Theoretical weight: 7.94 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CW78 (Residues: 36-105; Coverage: 65%)
Gene name: KLLA0_B06182g
Sequence domains: S25 ribosomal protein
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
40S ribosomal protein S26 Chain: a
Molecule details ›
Chain: a
Length: 100 amino acids
Theoretical weight: 11.45 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CS01 (Residues: 1-100; Coverage: 84%)
Gene name: KLLA0_D05115g
Sequence domains: Ribosomal protein S26e
Structure domains: Ribosomal protein S26e
40S ribosomal protein S27 Chain: b
Molecule details ›
Chain: b
Length: 82 amino acids
Theoretical weight: 8.88 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CNL2 (Residues: 1-82; Coverage: 100%)
Gene name: KLLA0_E11661g
Sequence domains: Ribosomal protein S27
Structure domains: Zn-binding ribosomal proteins
Small ribosomal subunit protein eS28 Chain: c
Molecule details ›
Chain: c
Length: 63 amino acids
Theoretical weight: 7.07 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: P33285 (Residues: 5-67; Coverage: 94%)
Gene names: KLLA0F20383g, RPS28
Sequence domains: Ribosomal protein S28e
Structure domains: Nucleic acid-binding proteins
Small ribosomal subunit protein uS14 Chain: d
Molecule details ›
Chain: d
Length: 53 amino acids
Theoretical weight: 6.32 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CPG3 (Residues: 4-56; Coverage: 95%)
Gene names: KLLA0E05071g, RPS29
Sequence domains: Ribosomal protein S14p/S29e
Structure domains: 30s Ribosomal Protein S14; Chain N
40S ribosomal protein S30 Chain: e
Molecule details ›
Chain: e
Length: 55 amino acids
Theoretical weight: 6.33 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CUH5 (Residues: 9-63; Coverage: 87%)
Gene name: KLLA0_C04809g
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein eS31 Chain: f
Molecule details ›
Chain: f
Length: 69 amino acids
Theoretical weight: 7.96 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: P69061 (Residues: 82-150; Coverage: 46%)
Gene names: KLLA0D18304g, ubi3
Sequence domains: Ribosomal protein S27a
Structure domains: N-terminal domain of TfIIb
Asc1 Chain: g
Molecule details ›
Chain: g
Length: 324 amino acids
Theoretical weight: 35.61 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CNI7 (Residues: 3-326; Coverage: 99%)
Gene name: KLLA0_E12277g
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1780 nucleotides
Theoretical weight: 573.51 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
Cricket paralysis virus IRES RNA Chain: i
Molecule details ›
Chain: i
Length: 192 nucleotides
Theoretical weight: 61.46 KDa
Sequence domains: Cripavirus internal ribosome entry site (IRES)

Ligands and Environments

2 bound ligands:
Ligand MG 80 x MG
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-8124

Quick links

Citations

16 review citations

Noncanonical Translation Initiation in Eukaryotes.
Kwan et al. (2019)
15 more

5 mentions without citation

Structural characterization of ribosome recruitment and translocation by type IV IRES.
Murray et al. (2016)
4 more