› 6q95

Electron Microscopy
3.7Å resolution

Structure of tmRNA SmpB bound in A site of T. thermophilus 70S ribosome

Released:
DOI: 10.2210/pdb6q95/pdb
PDB entry 6q95 coloured by chain, front view.
PDB entry 6q95 coloured by chain, side view.
PDB entry 6q95 coloured by chain, top view.
Source organisms:
Primary publication:
How a circularized tmRNA moves through the ribosome.
Rae CD, Gordiyenko Y, Ramakrishnan V
Science 363 740-744 (2019)
PMID: 30765567
Related structures: EMD-4475

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 61-mer (preferred)
PDBe Complex ID:
PDB-CPX-216286 (preferred)
Entry contents:
53 distinct polypeptide molecules
7 distinct RNA molecules
Macromolecules (60 distinct):
Small ribosomal subunit protein uS2 Chain: g
Molecule details ›
Chain: g
Length: 235 amino acids
Theoretical weight: 27.12 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 7-241; Coverage: 92%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: h
Molecule details ›
Chain: h
Length: 207 amino acids
Theoretical weight: 22.98 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 2-208; Coverage: 87%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: i
Small ribosomal subunit protein uS5 Chain: j
Small ribosomal subunit protein bS6 Chain: k
Small ribosomal subunit protein uS7 Chain: l
Small ribosomal subunit protein uS8 Chain: m
Small ribosomal subunit protein uS9 Chain: n
Small ribosomal subunit protein uS10 Chain: o
Small ribosomal subunit protein uS11 Chain: p
Small ribosomal subunit protein uS12 Chain: q
Small ribosomal subunit protein uS13 Chain: r
Small ribosomal subunit protein uS14 Chain: s
Small ribosomal subunit protein uS15 Chain: t
Small ribosomal subunit protein bS16 Chain: u
Small ribosomal subunit protein uS17 Chain: v
Small ribosomal subunit protein bS18 Chain: w
Small ribosomal subunit protein uS19 Chain: x
Small ribosomal subunit protein bS20 Chain: y
Small ribosomal subunit protein bTHX Chain: z
Large ribosomal subunit protein bL27 Chain: W
Large ribosomal subunit protein bL28 Chain: X
Large ribosomal subunit protein uL29 Chain: Y
Large ribosomal subunit protein uL30 Chain: Z
Large ribosomal subunit protein bL31 Chain: a
Large ribosomal subunit protein bL32 Chain: b
Large ribosomal subunit protein bL33 Chain: c
Large ribosomal subunit protein bL34 Chain: d
Large ribosomal subunit protein bL35 Chain: e
Large ribosomal subunit protein uL1 Chain: A
Large ribosomal subunit protein uL2 Chain: B
Large ribosomal subunit protein uL3 Chain: C
Large ribosomal subunit protein uL4 Chain: D
Large ribosomal subunit protein uL5 Chain: E
Large ribosomal subunit protein uL6 Chain: F
Large ribosomal subunit protein bL9 Chain: G
Large ribosomal subunit protein uL13 Chain: J
Large ribosomal subunit protein uL14 Chain: K
Large ribosomal subunit protein uL15 Chain: L
Large ribosomal subunit protein uL16 Chain: M
Large ribosomal subunit protein bL17 Chain: N
Large ribosomal subunit protein uL18 Chain: O
Large ribosomal subunit protein bL19 Chain: P
Large ribosomal subunit protein bL20 Chain: Q
Large ribosomal subunit protein bL21 Chain: R
Large ribosomal subunit protein uL22 Chain: S
Large ribosomal subunit protein uL23 Chain: T
Large ribosomal subunit protein uL24 Chain: U
Large ribosomal subunit protein bL25 Chain: V
SsrA-binding protein Chain: 5
Nascent peptide MET-ALA Chain: 6
Large ribosomal subunit protein bL36 Chain: f
50S RIBOSOMAL PROTEIN L10 AND L11 Chains: H, I
16S ribosomal RNA Chain: 2
tRNA-fMet Chain: 7
tRNA-Phe Chain: 8
Messenger RNA Chain: 9
23S ribosomal RNA Chain: 1
5S ribosomal RNA Chain: 3
transfer-messenger RNA (tmRNA) Chain: 4

Ligands and Environments

2 bound ligands:
Ligand MG 637 x MG
Ligand ZN 3 x ZN
1 modified residue:
Ligand 5MU 1 x 5MU

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.7Å
Relevant EMDB volumes: EMD-4475
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Quality controls induced by aberrant translation.
Inada T. (2020)
5 more

2 mentions without citation

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.
Gerovac et al. (2021)
1 more