› 4l71

X-ray diffraction
3.9Å resolution

Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-A on the Ribosome

Released:
DOI: 10.2210/pdb4l71/pdb
Model geometry
Fit model/data
PDB entry 4l71 coloured by chain, front view.
PDB entry 4l71 coloured by chain, side view.
PDB entry 4l71 coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops.
Maehigashi T, Dunkle JA, Miles SJ, Dunham CM
Proc Natl Acad Sci U S A 111 12740-5 (2014)
PMID: 25128388

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 56-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143714 (preferred)
Entry contents:
49 distinct polypeptide molecules
7 distinct RNA molecules
Macromolecules (56 distinct):
Small ribosomal subunit protein uS2 Chains: QB, XB
Molecule details ›
Chains: QB, XB
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: QC, XC
Molecule details ›
Chains: QC, XC
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
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
Large ribosomal subunit protein uL2 Chains: RD, YD
Large ribosomal subunit protein uL3 Chains: RE, YE
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
16S ribosomal RNA Chains: QA, XA
23S ribosomal RNA Chains: RA, YA
5S ribosomal RNA Chains: RB, YB
P-site tRNA fMet Chains: QV, XV
A-site ASL SufA6 Chains: QX, XX
Messenger RNA Chains: QY, XY
tRNA acceptor end mimic Chains: Z6, Z8

Ligands and Environments

3 bound ligands:
Ligand MG 676 x MG
Ligand PAR 2 x PAR
Ligand ZN 6 x ZN
2 modified residues:
Ligand 1MG 2 x 1MG
Ligand PPU 2 x PPU

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 210.241Å b: 446.1Å c: 623.316Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.235 0.278

Quick links

Citations

13 review citations

The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis.
Schimmel P. (2018)
12 more

1 mention without citation

Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops.
Maehigashi et al. (2014)