› 9gr1

Electron Microscopy
3.17Å resolution

E. coli 70S-TEC complex in delivery state

Released:
DOI: 10.2210/pdb9gr1/pdb
PDB entry 9gr1 coloured by chain, front view.
PDB entry 9gr1 coloured by chain, side view.
PDB entry 9gr1 coloured by chain, top view.
Source organism: Escherichia coli BL21(DE3)
Primary publication:
Molecular basis of mRNA delivery to the bacterial ribosome.
Webster MW, Chauvier A, Rahil H, Graziadei A, Charles K, Miropolskaya N, Takacs M, Saint-André C, Rappsilber J, Walter NG, Weixlbaumer A
Science 386 eado8476 (2024)
PMID: 39607923
Related structures: EMD-51517

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-293458 (preferred)
Entry contents:
48 distinct polypeptide molecules
7 distinct RNA molecules
Macromolecules (55 distinct):
Large ribosomal subunit protein bL33 Chain: 0
Molecule details ›
Chain: 0
Length: 55 amino acids
Theoretical weight: 6.39 KDa
Source organism: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A7N9 (Residues: 1-55; Coverage: 100%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 1
Molecule details ›
Chain: 1
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 2
Large ribosomal subunit protein bL36A Chain: 3
Small ribosomal subunit protein uS2 Chain: B
Small ribosomal subunit protein uS3 Chain: C
Small ribosomal subunit protein uS4 Chain: D
Small ribosomal subunit protein uS5 Chain: E
Small ribosomal subunit protein bS6 Chain: F
Small ribosomal subunit protein uS7 Chain: G
Small ribosomal subunit protein uS8 Chain: H
Small ribosomal subunit protein uS9 Chain: I
Small ribosomal subunit protein uS10 Chain: J
Small ribosomal subunit protein uS11 Chain: K
Small ribosomal subunit protein uS12 Chain: L
Small ribosomal subunit protein uS13 Chain: M
Small ribosomal subunit protein uS14 Chain: N
Small ribosomal subunit protein uS15 Chain: O
Small ribosomal subunit protein bS16 Chain: P
Small ribosomal subunit protein uS17 Chain: Q
Small ribosomal subunit protein bS18 Chain: R
Small ribosomal subunit protein uS19 Chain: S
Small ribosomal subunit protein bS20 Chain: T
Small ribosomal subunit protein bS21 Chain: U
Large ribosomal subunit protein uL2 Chain: c
Large ribosomal subunit protein uL3 Chain: d
Large ribosomal subunit protein uL4 Chain: e
Large ribosomal subunit protein uL5 Chain: f
Large ribosomal subunit protein uL6 Chain: g
Large ribosomal subunit protein bL9 Chain: h
Large ribosomal subunit protein uL13 Chain: i
Large ribosomal subunit protein uL14 Chain: j
Large ribosomal subunit protein uL15 Chain: k
Large ribosomal subunit protein uL16 Chain: l
Large ribosomal subunit protein bL17 Chain: m
Large ribosomal subunit protein uL18 Chain: n
Large ribosomal subunit protein bL19 Chain: o
Large ribosomal subunit protein bL20 Chain: p
Large ribosomal subunit protein bL21 Chain: q
Large ribosomal subunit protein uL22 Chain: r
Large ribosomal subunit protein uL23 Chain: s
Large ribosomal subunit protein uL24 Chain: t
Large ribosomal subunit protein bL25 Chain: u
Large ribosomal subunit protein bL27 Chain: v
Large ribosomal subunit protein bL28 Chain: w
Large ribosomal subunit protein uL29 Chain: x
Large ribosomal subunit protein uL30 Chain: y
Large ribosomal subunit protein bL32 Chain: z
16S ribosomal RNA Chain: A
mRNA in ribosome channel Chain: X
Phe-NH-tRNA(Phe) A-site Chain: Z
23S ribosomal RNA Chain: a
5S ribosomal RNA Chain: b
mRNA in SD-aSD duplex Chain: 4
tRNA(fmet) P-site Chain: Y

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand K 168 x K
Ligand MG 360 x MG
Ligand PHE 1 x PHE
22 modified residues:
Ligand PSU 14 x PSU
Ligand G7M 2 x G7M
Ligand 2MG 5 x 2MG
Ligand 5MC 3 x 5MC
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6
Ligand D2T 1 x D2T
Ligand 4SU 2 x 4SU
Ligand H2U 4 x H2U
Ligand MIA 1 x MIA
Ligand 7MG 1 x 7MG
Ligand 3AU 1 x 3AU
Ligand 5MU 4 x 5MU
Ligand 1MG 1 x 1MG
Ligand 6MZ 2 x 6MZ
Ligand 3TD 1 x 3TD
Ligand OMG 1 x OMG
Ligand OMC 2 x OMC
Ligand 2MA 1 x 2MA
Ligand OMU 1 x OMU
Ligand 4D4 1 x 4D4

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.17Å
Relevant EMDB volumes: EMD-51517

Quick links

Citations

1 citations in other articles

Bacterial Rps3 counters oxidative and UV stress by recognizing and processing AP-sites on mRNA via a novel mechanism.
Afsar et al. (2024)