› 5j3c

X-ray diffraction
3.04Å resolution

Thermus thermophilus 70S termination complex containing E. coli RF1

Released:
DOI: 10.2210/pdb5j3c/pdb
Model geometry
Fit model/data
Data not analysed
PDB entry 5j3c coloured by chain, front view.
PDB entry 5j3c coloured by chain, side view.
PDB entry 5j3c coloured by chain, top view.
Source organisms:
Primary publication:
Uniformity of Peptide Release Is Maintained by Methylation of Release Factors.
Pierson WE, Hoffer ED, Keedy HE, Simms CL, Dunham CM, Zaher HS
Cell Rep 17 11-18 (2016)
PMID: 27681416

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
PDBe Complex ID:
PDB-CPX-302234 (preferred)
Entry contents:
50 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (55 distinct):
Large ribosomal subunit protein uL2 Chains: RD, YD
Molecule details ›
Chains: RD, YD
Length: 276 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 1-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: RE, YE
Molecule details ›
Chains: RE, YE
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: RF, YF
Large ribosomal subunit protein uL5 Chains: RG, YG
Large ribosomal subunit protein uL6 Chains: RH, YH
Large ribosomal subunit protein bL9 Chains: RI, YI
Large ribosomal subunit protein uL13 Chains: RN, YN
Large ribosomal subunit protein uL14 Chains: RO, YO
Large ribosomal subunit protein uL15 Chains: RP, YP
Large ribosomal subunit protein uL16 Chains: RQ, YQ
Large ribosomal subunit protein bL17 Chains: RR, YR
Large ribosomal subunit protein uL18 Chains: RS, YS
Large ribosomal subunit protein bL19 Chains: RT, YT
Large ribosomal subunit protein bL20 Chains: RU, YU
Large ribosomal subunit protein bL21 Chains: RV, YV
Large ribosomal subunit protein uL22 Chains: RW, YW
Large ribosomal subunit protein uL23 Chains: RX, YX
Large ribosomal subunit protein uL24 Chains: RY, YY
Large ribosomal subunit protein bL25 Chains: RZ, YZ
Large ribosomal subunit protein bL27 Chains: R0, Y0
Large ribosomal subunit protein bL28 Chains: R1, Y1
Large ribosomal subunit protein uL29 Chains: R2, Y2
Large ribosomal subunit protein uL30 Chains: R3, Y3
Large ribosomal subunit protein bL31 Chains: R4, Y4
Large ribosomal subunit protein bL32 Chains: R5, Y5
Large ribosomal subunit protein bL33 Chains: R6, Y6
Large ribosomal subunit protein bL34 Chains: R7, Y7
Large ribosomal subunit protein bL35 Chains: R8, Y8
Large ribosomal subunit protein bL36 Chains: R9, Y9
Small ribosomal subunit protein uS2 Chains: QB, XB
Small ribosomal subunit protein uS3 Chains: QC, XC
Small ribosomal subunit protein uS4 Chains: QD, XD
Small ribosomal subunit protein uS5 Chains: QE, XE
Small ribosomal subunit protein bS6 Chains: QF, XF
Small ribosomal subunit protein uS7 Chains: QG, XG
Small ribosomal subunit protein uS8 Chains: QH, XH
Small ribosomal subunit protein uS9 Chains: QI, XI
Small ribosomal subunit protein uS10 Chains: QJ, XJ
Small ribosomal subunit protein uS11 Chains: QK, XK
Small ribosomal subunit protein uS12 Chains: QL, XL
Small ribosomal subunit protein uS13 Chains: QM, XM
Small ribosomal subunit protein uS14 Chains: QN, XN
Small ribosomal subunit protein uS15 Chains: QO, XO
Small ribosomal subunit protein bS16 Chains: QP, XP
Small ribosomal subunit protein uS17 Chains: QQ, XQ
Small ribosomal subunit protein bS18 Chains: QR, XR
Small ribosomal subunit protein uS19 Chains: QS, XS
Small ribosomal subunit protein bS20 Chains: QT, XT
Small ribosomal subunit protein bTHX Chains: QU, XU
Peptide chain release factor RF1 Chains: QY, XY
23S ribosomal RNA Chains: RA, YA
5S ribosomal RNA Chains: RB, YB
16S ribosomal RNA Chains: QA, XA
P-site tRNA fMet Chains: QV, XV
Messenger RNA Chains: QX, XX

Ligands and Environments

3 bound ligands:
Ligand MG 2436 x MG
Ligand ZN 12 x ZN
Ligand SF4 2 x SF4
13 modified residues:
Ligand PSU 8 x PSU
Ligand 5MU 4 x 5MU
Ligand 4OC 4 x 4OC
Ligand 5MC 12 x 5MC
Ligand OMG 2 x OMG
Ligand 2MA 2 x 2MA
Ligand 2MU 2 x 2MU
Ligand 7MG 2 x 7MG
Ligand M2G 2 x M2G
Ligand 2MG 2 x 2MG
Ligand UR3 2 x UR3
Ligand MA6 4 x MA6
Ligand 0TD 2 x 0TD

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 209.51Å b: 450.89Å c: 622.07Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.248 0.246 0.278
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Translation Termination and Ribosome Recycling in Eukaryotes.
Hellen CUT. (2018)
2 more

4 mentions without citation

An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome.
Florin et al. (2017)
3 more