› 4v7h

Electron Microscopy
8.9Å resolution

Structure of the 80S rRNA and proteins and P/E tRNA for eukaryotic ribosome based on cryo-EM map of Thermomyces lanuginosus ribosome at 8.9A resolution

Released:
DOI: 10.2210/pdb4v7h/pdb
PDB entry 4v7h coloured by chain, front view.
PDB entry 4v7h coloured by chain, side view.
PDB entry 4v7h coloured by chain, top view.
Source organism: Thermomyces lanuginosus
Primary publication:
Comprehensive molecular structure of the eukaryotic ribosome.
Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E, Sali A, Harvey SC, Frank J
Structure 17 1591-1604 (2009)
PMID: 20004163
Related structures: EMD-1345

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
PDBe Complex ID:
PDB-CPX-165267 (preferred)
Entry contents:
48 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (53 distinct):
40S ribosomal protein S0(A) Chain: AB
Molecule details ›
Chain: AB
Length: 193 amino acids
Theoretical weight: 21.24 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S3 Chain: AC
Molecule details ›
Chain: AC
Length: 188 amino acids
Theoretical weight: 20.93 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S9(A) Chain: AD
Molecule details ›
Chain: AD
Length: 158 amino acids
Theoretical weight: 18.42 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S2 Chain: AE
Molecule details ›
Chain: AE
Length: 162 amino acids
Theoretical weight: 17.15 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S5 Chain: AG
Molecule details ›
Chain: AG
Length: 186 amino acids
Theoretical weight: 20.73 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S22(A) Chain: AH
Molecule details ›
Chain: AH
Length: 125 amino acids
Theoretical weight: 14.1 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S16(A) Chain: AI
Molecule details ›
Chain: AI
Length: 138 amino acids
Theoretical weight: 15.39 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S20 Chain: AJ
Molecule details ›
Chain: AJ
Length: 96 amino acids
Theoretical weight: 10.98 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S14(A) Chain: AK
Molecule details ›
Chain: AK
Length: 125 amino acids
Theoretical weight: 13.19 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S23(A) Chain: AL
Molecule details ›
Chain: AL
Length: 118 amino acids
Theoretical weight: 12.88 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S18 Chain: AM
Molecule details ›
Chain: AM
Length: 130 amino acids
Theoretical weight: 15.3 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S29(A) Chain: AN
Molecule details ›
Chain: AN
Length: 50 amino acids
Theoretical weight: 5.95 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S13 Chain: AO
Molecule details ›
Chain: AO
Length: 84 amino acids
Theoretical weight: 9.84 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S11 Chain: AQ
Molecule details ›
Chain: AQ
Length: 80 amino acids
Theoretical weight: 9.13 KDa
Source organism: Thermomyces lanuginosus
40S ribosomal protein S15 Chain: AS
Molecule details ›
Chain: AS
Length: 71 amino acids
Theoretical weight: 7.86 KDa
Source organism: Thermomyces lanuginosus
RACK1 protein Chain: AR
Molecule details ›
Chain: AR
Length: 313 amino acids
Theoretical weight: 34.21 KDa
Source organism: Thermomyces lanuginosus
s19e protein Chain: AT
Molecule details ›
Chain: AT
Length: 141 amino acids
Theoretical weight: 15.66 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L32 Chain: B0
Molecule details ›
Chain: B0
Length: 109 amino acids
Theoretical weight: 12.5 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L39 Chain: B1
Molecule details ›
Chain: B1
Length: 48 amino acids
Theoretical weight: 6.04 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L30e Chain: B2
Molecule details ›
Chain: B2
Length: 98 amino acids
Theoretical weight: 10.69 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein LP0 Chain: B8
Molecule details ›
Chain: B8
Length: 118 amino acids
Theoretical weight: 13.44 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L43 Chain: B9
Molecule details ›
Chain: B9
Length: 72 amino acids
Theoretical weight: 7.74 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L1 Chain: BA
Molecule details ›
Chain: BA
Length: 213 amino acids
Theoretical weight: 24.01 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L2 Chain: BB
Molecule details ›
Chain: BB
Length: 243 amino acids
Theoretical weight: 26.2 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L3 Chain: BC
Molecule details ›
Chain: BC
Length: 362 amino acids
Theoretical weight: 40.95 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L4(B) Chain: BD
Molecule details ›
Chain: BD
Length: 257 amino acids
Theoretical weight: 27.67 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L5 Chain: BE
Molecule details ›
Chain: BE
Length: 237 amino acids
Theoretical weight: 27.06 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L7(A) Chain: BF
Molecule details ›
Chain: BF
Length: 213 amino acids
Theoretical weight: 22.06 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L8(A) Chain: BG
Molecule details ›
Chain: BG
Length: 113 amino acids
Theoretical weight: 12.03 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L9(A) Chain: BH
Molecule details ›
Chain: BH
Length: 179 amino acids
Theoretical weight: 20.16 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L10 Chain: BI
Molecule details ›
Chain: BI
Length: 165 amino acids
Theoretical weight: 18.89 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L11(B) Chain: BJ
Molecule details ›
Chain: BJ
Length: 151 amino acids
Theoretical weight: 17.02 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L12 Chain: BK
Molecule details ›
Chain: BK
Length: 138 amino acids
Theoretical weight: 14.8 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L15(A) Chain: BL
Molecule details ›
Chain: BL
Length: 192 amino acids
Theoretical weight: 22.9 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L16(A) Chain: BM
Molecule details ›
Chain: BM
Length: 178 amino acids
Theoretical weight: 18.66 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L17(A) Chain: BN
Molecule details ›
Chain: BN
Length: 150 amino acids
Theoretical weight: 16.83 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L18(A) Chain: BO
Molecule details ›
Chain: BO
Length: 121 amino acids
Theoretical weight: 13.22 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L19 Chain: BP
Molecule details ›
Chain: BP
Length: 176 amino acids
Theoretical weight: 18.69 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L21(A) Chain: BQ
Molecule details ›
Chain: BQ
Length: 116 amino acids
Theoretical weight: 12.69 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L23 Chain: BR
Molecule details ›
Chain: BR
Length: 131 amino acids
Theoretical weight: 13.98 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L24(A) Chain: BS
Molecule details ›
Chain: BS
Length: 45 amino acids
Theoretical weight: 5.23 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L25 Chain: BT
Molecule details ›
Chain: BT
Length: 80 amino acids
Theoretical weight: 9.15 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L26(A) Chain: BU
Molecule details ›
Chain: BU
Length: 116 amino acids
Theoretical weight: 13.02 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L28 Chain: BV
Molecule details ›
Chain: BV
Length: 142 amino acids
Theoretical weight: 15.91 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L31(A) Chain: BW
Molecule details ›
Chain: BW
Length: 79 amino acids
Theoretical weight: 9.42 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L35 Chain: BX
Molecule details ›
Chain: BX
Length: 86 amino acids
Theoretical weight: 8.64 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L37(A) Chain: BY
Molecule details ›
Chain: BY
Length: 52 amino acids
Theoretical weight: 5.77 KDa
Source organism: Thermomyces lanuginosus
60S ribosomal protein L42 Chain: BZ
Molecule details ›
Chain: BZ
Length: 92 amino acids
Theoretical weight: 10.71 KDa
Source organism: Thermomyces lanuginosus
18S Ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 1761 nucleotides
Theoretical weight: 567.33 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
P/E tRNA Chain: A7
Molecule details ›
Chain: A7
Length: 76 nucleotides
Theoretical weight: 24.89 KDa
Sequence domains: tRNA
5S ribosomal RNA Chain: B3
Molecule details ›
Chain: B3
Length: 113 nucleotides
Theoretical weight: 36.34 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: B4
Molecule details ›
Chain: B4
Length: 157 nucleotides
Theoretical weight: 50.37 KDa
Sequence domains: 5.8S ribosomal RNA
26S ribosomal RNA Chain: B5
Molecule details ›
Chain: B5
Length: 3170 nucleotides
Theoretical weight: 1024.35 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA

Ligands and Environments

No bound ligands
11 modified residues:
Ligand 2MG 1 x 2MG
Ligand H2U 2 x H2U
Ligand M2G 1 x M2G
Ligand OMC 1 x OMC
Ligand OMG 1 x OMG
Ligand YYG 1 x YYG
Ligand PSU 2 x PSU
Ligand 5MC 2 x 5MC
Ligand 7MG 1 x 7MG
Ligand 5MU 1 x 5MU
Ligand 1MA 1 x 1MA

Experiments and Validation Details

Entry percentile scores
Resolution: 8.9Å
Relevant EMDB volumes: EMD-1345

Quick links

Citations

23 review citations

Molecular mechanism of scanning and start codon selection in eukaryotes.
Hinnebusch AG. (2011)
22 more

4 mentions without citation

The Mechanisms of Action of Ribosome-Targeting Peptide Antibiotics.
Polikanov et al. (2018)
3 more