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› 4v83

X-ray diffraction
3.5Å resolution

Crystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to the 70S ribosome.

Released:
DOI: 10.2210/pdb4v83/pdb
Model geometry
Fit model/data
PDB entry 4v83 coloured by chain, front view.
PDB entry 4v83 coloured by chain, side view.
PDB entry 4v83 coloured by chain, top view.
Source organism: Thermus thermophilus HB27
Primary publication:
Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.
Zhu J, Korostelev A, Costantino DA, Donohue JP, Noller HF, Kieft JS
Proc Natl Acad Sci U S A 108 1839-44 (2011)
PMID: 21245352

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-302873 (preferred)
Entry contents:
49 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (53 distinct):
Small ribosomal subunit protein uS2 Chains: AB, CB
Molecule details ›
Chains: AB, CB
Length: 234 amino acids
Theoretical weight: 26.99 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62662 (Residues: 7-240; Coverage: 91%)
Gene names: TT_C0509, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: AC, CC
Molecule details ›
Chains: AC, CC
Length: 206 amino acids
Theoretical weight: 22.86 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62663 (Residues: 2-207; Coverage: 86%)
Gene names: TT_C1322, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: AD, CD
Small ribosomal subunit protein uS5 Chains: AE, CE
Small ribosomal subunit protein bS6 Chains: AF, CF
Small ribosomal subunit protein uS7 Chains: AG, CG
Small ribosomal subunit protein uS8 Chains: AH, CH
Small ribosomal subunit protein uS9 Chains: AI, CI
Small ribosomal subunit protein uS10 Chains: AJ, CJ
Small ribosomal subunit protein uS11 Chains: AK, CK
Small ribosomal subunit protein uS12 Chains: AL, CL
Small ribosomal subunit protein uS13 Chains: AM, CM
Small ribosomal subunit protein uS14 Chains: AN, CN
Small ribosomal subunit protein uS15 Chains: AO, CO
Small ribosomal subunit protein bS16 Chains: AP, CP
Small ribosomal subunit protein uS17 Chains: AQ, CQ
Small ribosomal subunit protein bS18 Chains: AR, CR
Small ribosomal subunit protein uS19 Chains: AS, CS
Small ribosomal subunit protein bS20 Chains: AT, CT
Small ribosomal subunit protein bTHX Chains: AU, CU
Large ribosomal subunit protein uL2 Chains: BC, DC
Large ribosomal subunit protein uL3 Chains: BD, DD
Large ribosomal subunit protein uL4 Chains: BE, DE
Large ribosomal subunit protein uL5 Chains: BF, DF
Large ribosomal subunit protein uL6 Chains: BG, DG
Large ribosomal subunit protein bL9 Chains: BH, DH
Large ribosomal subunit protein uL10 Chains: BI, DI
Large ribosomal subunit protein uL13 Chains: BJ, DJ
Large ribosomal subunit protein uL14 Chains: BK, DK
Large ribosomal subunit protein uL15 Chains: BL, DL
Large ribosomal subunit protein uL16 Chains: BM, DM
Large ribosomal subunit protein bL17 Chains: BN, DN
Large ribosomal subunit protein uL18 Chains: BO, DO
Large ribosomal subunit protein bL19 Chains: BP, DP
Large ribosomal subunit protein bL20 Chains: BQ, DQ
Large ribosomal subunit protein bL21 Chains: BR, DR
Large ribosomal subunit protein uL22 Chains: BS, DS
Large ribosomal subunit protein uL23 Chains: BT, DT
Large ribosomal subunit protein uL24 Chains: BU, DU
Large ribosomal subunit protein bL25 Chains: BV, DV
Large ribosomal subunit protein bL27 Chains: BW, DW
Large ribosomal subunit protein bL28 Chains: BX, DX
Large ribosomal subunit protein uL29 Chains: BY, DY
Large ribosomal subunit protein uL30 Chains: BZ, DZ
Large ribosomal subunit protein bL31 Chains: B1, D1
Large ribosomal subunit protein bL32 Chains: B2, D2
Large ribosomal subunit protein bL33 Chains: B3, D3
Large ribosomal subunit protein bL34 Chains: B4, D4
Large ribosomal subunit protein bL35 Chains: B5, D5
16S ribosomal RNA Chains: AA, CA
domain 3 of PSIC IGR IRES RNA Chains: AV, CV
23S ribosomal RNA Chains: BA, DA
5S ribosomal RNA Chains: BB, DB

Ligands and Environments

2 bound ligands:
Ligand MG 2657 x MG
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 211.94Å b: 455.59Å c: 618.02Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.233 0.264

Quick links

Citations

10 review citations

Viral RNA structure-based strategies to manipulate translation.
Jaafar et al. (2019)
9 more

1 mention without citation

Mg2+ ions: do they bind to nucleobase nitrogens?
Leonarski et al. (2017)