› 8b01

Electron Microscopy
3.03Å resolution

Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in a nanodisc

Released:
DOI: 10.2210/pdb8b01/pdb
PDB entry 8b01 coloured by chain, front view.
PDB entry 8b01 coloured by chain, side view.
PDB entry 8b01 coloured by chain, top view.
Source organisms:
Primary publication:
Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter.
Davies JS, Currie MJ, North RA, Scalise M, Wright JD, Copping JM, Remus DM, Gulati A, Morado DR, Jamieson SA, Newton-Vesty MC, Abeysekera GS, Ramaswamy S, Friemann R, Wakatsuki S, Allison JR, Indiveri C, Drew D, Mace PD, Dobson RCJ
OpenAccess logo Nat Commun 14 1120 (2023)
PMID: 36849793
Related structures: EMD-15775

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-110291 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
TRAP transporter small permease protein Chain: A
Molecule details ›
Chain: A
Length: 170 amino acids
Theoretical weight: 19.75 KDa
Source organism: Photobacterium profundum SS9
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6LPW0 (Residues: 1-169; Coverage: 99%)
Gene names: PBPRA2280, VC1778
Sequence domains: Tripartite ATP-independent periplasmic transporters, DctQ component
TRAP transporter large permease protein Chain: B
Molecule details ›
Chain: B
Length: 427 amino acids
Theoretical weight: 45.57 KDa
Source organism: Photobacterium profundum SS9
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6LPW1 (Residues: 1-426; Coverage: 100%)
Gene names: PBPRA2279, SMB20297
Sequence domains: Tripartite ATP-independent periplasmic transporter, DctM component
SabA N-terminal extracellular adhesion domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 510 amino acids
Theoretical weight: 54.87 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli
UniProt:
  • Canonical: B5Z8H1 (Residues: 226-447, 448-470; Coverage: 39%)
Gene names: HPG27_1120, hopQ
Sequence domains: SabA N-terminal extracellular adhesion domain

Ligands and Environments

7 bound ligands:
Ligand OCT 6 x OCT
Ligand PTY 2 x PTY
Ligand TWT 1 x TWT
Ligand D10 2 x D10
Ligand NA 2 x NA
Ligand TRD 1 x TRD
Ligand HEX 1 x HEX
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.03Å
Relevant EMDB volumes: EMD-15775
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Biochemical and structural basis of sialic acid utilization by gut microbes.
Bell et al. (2023)
1 other article

1 mention without citation

Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter.
Davies et al. (2023)