› 4v5o

X-ray diffraction
3.93Å resolution

CRYSTAL STRUCTURE OF THE EUKARYOTIC 40S RIBOSOMAL SUBUNIT IN COMPLEX WITH INITIATION FACTOR 1.

Released:
DOI: 10.2210/pdb4v5o/pdb
PDB entry 4v5o coloured by chain, front view.
PDB entry 4v5o coloured by chain, side view.
PDB entry 4v5o coloured by chain, top view.
Source organism: Tetrahymena thermophila
Primary publication:
Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.
Rabl J, Leibundgut M, Ataide SF, Haag A, Ban N
Science 331 730-6 (2011)
PMID: 21205638

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-107444 (preferred)
Entry contents:
34 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (35 distinct):
40S ribosomal protein S28e, putative Chains: A1, B1
Molecule details ›
Chains: A1, B1
Length: 68 amino acids
Theoretical weight: 7.63 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q234G5 (Residues: 1-68; Coverage: 100%)
Gene name: TTHERM_00105330
Sequence domains: Ribosomal protein S28e
40S ribosomal protein S8 Chains: A2, B2
Molecule details ›
Chains: A2, B2
Length: 208 amino acids
Theoretical weight: 24.25 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22AV0 (Residues: 1-208; Coverage: 100%)
Gene name: TTHERM_01151600
Sequence domains: Ribosomal protein S8e
RPS7E Chains: A3, B3
Molecule details ›
Chains: A3, B3
Length: 197 amino acids
Theoretical weight: 23.23 KDa
Source organism: Tetrahymena thermophila
Small ribosomal subunit protein eS1 Chains: A4, B4
Molecule details ›
Chains: A4, B4
Length: 265 amino acids
Theoretical weight: 29.71 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q23DE3 (Residues: 1-265; Coverage: 100%)
Gene name: TTHERM_00047480
Sequence domains: Ribosomal S3Ae family
40S ribosomal protein S26 Chains: A5, B5
Molecule details ›
Chains: A5, B5
Length: 119 amino acids
Theoretical weight: 13.84 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: E6PBU4 (Residues: 1-119; Coverage: 100%)
Sequence domains: Ribosomal protein S26e
40S ribosomal protein S27 Chains: A6, B6
Molecule details ›
Chains: A6, B6
Length: 81 amino acids
Theoretical weight: 9.25 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22CK0 (Residues: 1-81, 1-53; Coverage: 65%)
Gene name: TTHERM_01043090
Sequence domains: Ribosomal protein S27
Plectin/eS10 N-terminal domain-containing protein Chains: A7, B7
Molecule details ›
Chains: A7, B7
Length: 162 amino acids
Theoretical weight: 18.61 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q24F70 (Residues: 1-162; Coverage: 100%)
Gene name: TTHERM_01128560
Sequence domains: Plectin/S10 domain
RPS25E Chains: A8, B8
Molecule details ›
Chains: A8, B8
Length: 143 amino acids
Theoretical weight: 15.3 KDa
Source organism: Tetrahymena thermophila
RPS31E Chains: A9, B9
Molecule details ›
Chains: A9, B9
Length: 189 amino acids
Theoretical weight: 20.38 KDa
Source organism: Tetrahymena thermophila
RPS0E Chains: AB, BB
Molecule details ›
Chains: AB, BB
Length: 241 amino acids
Theoretical weight: 27.53 KDa
Source organism: Tetrahymena thermophila
40S ribosomal protein S3 Chains: AC, BC
Molecule details ›
Chains: AC, BC
Length: 243 amino acids
Theoretical weight: 27.58 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22AV9 (Residues: 1-243; Coverage: 100%)
Gene name: TTHERM_01151500
Sequence domains:
Small ribosomal subunit protein uS4 N-terminal domain-containing protein Chains: AD, BD
Molecule details ›
Chains: AD, BD
Length: 181 amino acids
Theoretical weight: 21.19 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q230V2 (Residues: 58-238; Coverage: 76%)
Gene name: TTHERM_00434070
Sequence domains:
S5 DRBM domain-containing protein Chains: AE, BE
Molecule details ›
Chains: AE, BE
Length: 296 amino acids
Theoretical weight: 33.74 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q23KG1 (Residues: 1-296; Coverage: 100%)
Gene name: TTHERM_00193740
Sequence domains:
EIF1 Chains: AF, BF
Molecule details ›
Chains: AF, BF
Length: 101 amino acids
Theoretical weight: 11.96 KDa
Source organism: Tetrahymena thermophila
Expression system: Escherichia coli
Small ribosomal subunit protein uS7 domain-containing protein Chains: AG, BG
Molecule details ›
Chains: AG, BG
Length: 200 amino acids
Theoretical weight: 22.51 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22WU7 (Residues: 1-200; Coverage: 100%)
Gene name: TTHERM_01386050
Sequence domains: Ribosomal protein S7p/S5e
40S ribosomal protein S15a Chains: AH, BH
Molecule details ›
Chains: AH, BH
Length: 130 amino acids
Theoretical weight: 14.93 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q238Q8 (Residues: 1-130; Coverage: 100%)
Gene name: TTHERM_00454080
Sequence domains: Ribosomal protein S8
RPS16E, 40S RIBOSOMAL PROTEIN RPS16E Chains: AI, BI
Molecule details ›
Chains: AI, BI
Length: 145 amino acids
Theoretical weight: 16.42 KDa
Source organism: Tetrahymena thermophila
Small ribosomal subunit protein uS10 domain-containing protein Chains: AJ, BJ
Molecule details ›
Chains: AJ, BJ
Length: 120 amino acids
Theoretical weight: 13.7 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22DC6 (Residues: 51-170; Coverage: 71%)
Gene name: TTHERM_00992760
Sequence domains: Ribosomal protein S10p/S20e
RPS14E Chains: AK, BK
Molecule details ›
Chains: AK, BK
Length: 151 amino acids
Theoretical weight: 16.4 KDa
Source organism: Tetrahymena thermophila
Small ribosomal subunit protein uS12 Chains: AL, BL
Molecule details ›
Chains: AL, BL
Length: 142 amino acids
Theoretical weight: 15.78 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P06147 (Residues: 1-142; Coverage: 100%)
Sequence domains: Ribosomal protein S12/S23
RPS18E Chains: AM, BM
Molecule details ›
Chains: AM, BM
Length: 155 amino acids
Theoretical weight: 17.8 KDa
Source organism: Tetrahymena thermophila
40S ribosomal protein S29 Chains: AN, BN
Molecule details ›
Chains: AN, BN
Length: 55 amino acids
Theoretical weight: 6.66 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22MB0 (Residues: 1-55, 1-53; Coverage: 96%)
Gene name: TTHERM_00037090
Sequence domains: Ribosomal protein S14p/S29e
RPS13E Chains: AO, BO
Molecule details ›
Chains: AO, BO
Length: 153 amino acids
Theoretical weight: 17.62 KDa
Source organism: Tetrahymena thermophila
40S ribosomal protein S29 Chains: AP, BP
Molecule details ›
Chains: AP, BP
Length: 149 amino acids
Theoretical weight: 17.13 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22MB0 (Residues: 34-44; Coverage: 20%)
Gene name: TTHERM_00037090
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chains: AQ, BQ
Molecule details ›
Chains: AQ, BQ
Length: 157 amino acids
Theoretical weight: 18.14 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22B78 (Residues: 1-157; Coverage: 100%)
Gene name: TTHERM_01109770
Sequence domains:
Receptor of activated kinase C 1A, component of 40S small ribosomal subunit Chains: AR, BR
Molecule details ›
Chains: AR, BR
Length: 343 amino acids
Theoretical weight: 38.52 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q24D42 (Residues: 1-343; Coverage: 100%)
Gene name: TTHERM_01113100
Sequence domains: WD domain, G-beta repeat
RPS15E Chains: AS, BS
Molecule details ›
Chains: AS, BS
Length: 144 amino acids
Theoretical weight: 15.91 KDa
Source organism: Tetrahymena thermophila
RPS19E Chains: AT, BT
Molecule details ›
Chains: AT, BT
Length: 155 amino acids
Theoretical weight: 17.77 KDa
Source organism: Tetrahymena thermophila
Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein Chains: AU, BU
Molecule details ›
Chains: AU, BU
Length: 126 amino acids
Theoretical weight: 13.83 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22W26 (Residues: 1-126; Coverage: 100%)
Gene name: TTHERM_00161060
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
RPS17E Chains: AV, BV
Molecule details ›
Chains: AV, BV
Length: 130 amino acids
Theoretical weight: 14.96 KDa
Source organism: Tetrahymena thermophila
Small ribosomal subunit protein eS4 Chains: AW, BW
Molecule details ›
Chains: AW, BW
Length: 260 amino acids
Theoretical weight: 29.64 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0C233 (Residues: 1-259; Coverage: 100%)
Sequence domains:
RPS30E Chains: AX, BX
Molecule details ›
Chains: AX, BX
Length: 80 amino acids
Theoretical weight: 9.25 KDa
Source organism: Tetrahymena thermophila
40S ribosomal protein S6 Chains: AY, BY
Molecule details ›
Chains: AY, BY
Length: 293 amino acids
Theoretical weight: 32.61 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: A4VD76 (Residues: 1-293; Coverage: 100%)
Gene name: TTHERM_00149798
Sequence domains: Ribosomal protein S6e
RPS21E Chains: AZ, BZ
Molecule details ›
Chains: AZ, BZ
Length: 97 amino acids
Theoretical weight: 10.7 KDa
Source organism: Tetrahymena thermophila
18S Ribosomal RNA Chains: AA, BA
Molecule details ›
Chains: AA, BA
Length: 1753 nucleotides
Theoretical weight: 565.19 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 184 x MG
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2
Unit cell:
a: 320.52Å b: 362.21Å c: 412.11Å
α: 90° β: 109.61° γ: 90°
R-values:
R R work R free
0.206 0.206 0.243
Expression system: Escherichia coli

Quick links

Citations

69 review citations

Ribosome biogenesis in the yeast Saccharomyces cerevisiae.
Woolford et al. (2013)
68 more

3 mentions without citation

Interdependent action of KH domain proteins Krr1 and Dim2 drive the 40S platform assembly.
Sturm et al. (2017)
2 more