PDBsum entry 6oqw

Membrane protein

PDB id: 6oqw

Contents

Protein chains

173 a.a.

510 a.a.

153 a.a.

136 a.a.

284 a.a.

458 a.a.

(+ 4 more) 77 a.a.

266 a.a.

Ligands

ATP ×3

ADP ×3

PO4

Metals

_MG ×5

PDB id:

6oqw

Name:

Membrane protein

Title:

E. Coli atp synthase state 3a

Structure:

Atp synthase subunit delta. Chain: w. Synonym: atp synthase f(1) sector subunit delta,f-type atpase subunit delta,f-atpase subunit delta. Engineered: yes. Atp synthase subunit alpha. Chain: c, b, a. Synonym: atp synthase f1 sector subunit alpha,f-atpase subunit alpha. Engineered: yes.

Source:

Escherichia coli. Organism_taxid: 562. Gene: atph, hmpref1611_00658. Expressed in: escherichia coli. Expression_system_taxid: 562. Escherichia coli 2-427-07_s4_c3. Organism_taxid: 1444266. Gene: atpa, ad31_4476. Gene: atpf, ad31_4478.

Authors:

A.G.Stewart,M.Sobti,J.L.Walshe

Key ref:

M.Sobti et al. (2020). Cryo-EM structures provide insight into how E. coli F₁F_o ATP synthase accommodates symmetry mismatch. Nat Commun, 11, 2615. PubMed id: 32457314 DOI: 10.1038/s41467-020-16387-2

Date:

29-Apr-19 Release date: 24-Jun-20

Protein chain

P0ABA4  (ATPD_ECOLI) -  ATP synthase subunit delta from Escherichia coli (strain K12)

Seq: 177 a.a.

Struc: 173 a.a.*

Protein chains

P0ABB0  (ATPA_ECOLI) -  ATP synthase subunit alpha from Escherichia coli (strain K12)

Seq: 513 a.a.

Struc: 510 a.a.

Protein chains

P0ABA0  (ATPF_ECOLI) -  ATP synthase subunit b from Escherichia coli (strain K12)

Seq: 156 a.a.

Struc: 153 a.a.*

Protein chain

P0A6E6  (ATPE_ECOLI) -  ATP synthase epsilon chain from Escherichia coli (strain K12)

Seq: 139 a.a.

Struc: 136 a.a.

Protein chain

P0ABA6  (ATPG_ECOLI) -  ATP synthase gamma chain from Escherichia coli (strain K12)

Seq: 287 a.a.

Struc: 284 a.a.*

Protein chains

P0ABB4  (ATPB_ECOLI) -  ATP synthase subunit beta from Escherichia coli (strain K12)

Seq: 460 a.a.

Struc: 458 a.a.*

Protein chains

P68699  (ATPL_ECOLI) -  ATP synthase subunit c from Escherichia coli (strain K12)

Seq: 79 a.a.

Struc: 77 a.a.

Protein chain

P0AB98  (ATP6_ECOLI) -  ATP synthase subunit a from Escherichia coli (strain K12)

Seq: 271 a.a.

Struc: 266 a.a.

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains C, B, A, F, E, D: E.C.7.1.2.2 - H(+)-transporting two-sector ATPase.
• Reaction: ATP + H2O + 4 H⁺(in) = ADP + phosphate + 5 H⁺(out)

ATP (Bound ligand (Het Group name = ATP) corresponds exactly) + H2O + 4 × H(+)(in) = ADP + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) + 5 × H(+)(out)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/s41467-020-16387-2

Nat Commun 11:2615 (2020)

PubMed id: 32457314

Cryo-EM structures provide insight into how E. coli F₁F_o ATP synthase accommodates symmetry mismatch.

M.Sobti, J.L.Walshe, D.Wu, R.Ishmukhametov, Y.C.Zeng, C.V.Robinson, R.M.Berry, A.G.Stewart.

ABSTRACT

F₁F_o ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the F_o motor generates rotation of the central stalk, inducing conformational changes in the F₁ motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1-3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of F_o associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F₁ and F_o motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the F_o motor.