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- PDB-9its: Chloroflexus aurantiacus ADP-bound ATP synthase, state 1 -

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Basic information

Entry
Database: PDB / ID: 9its
TitleChloroflexus aurantiacus ADP-bound ATP synthase, state 1
Components(ATP synthase ...) x 8
KeywordsMEMBRANE PROTEIN / ATP synthesis / proton channels / proton-motive force / proton translocation
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex / proton motive force-driven ATP synthesis / : / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding ...proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex / proton motive force-driven ATP synthesis / : / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit delta / ATP synthase subunit b / ATP synthase subunit c / ATP synthase subunit a
Similarity search - Component
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsZhang, X. / Wu, J. / Xu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171227, 31870740,31570738 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structure of ATP synthase from an early photosynthetic bacterium .
Authors: Xin Zhang / Jingyi Wu / Zhenzhen Min / Jiamao Wang / Xin Hong / Xinkai Pei / Zihe Rao / Xiaoling Xu /
Abstract: F-type ATP synthase (FF) catalyzes proton motive force-driven ATP synthesis in mitochondria, chloroplasts, and bacteria. Different from the mitochondrial and bacterial enzymes, FF from photosynthetic ...F-type ATP synthase (FF) catalyzes proton motive force-driven ATP synthesis in mitochondria, chloroplasts, and bacteria. Different from the mitochondrial and bacterial enzymes, FF from photosynthetic organisms have evolved diverse structural and mechanistic details to adapt to the light-dependent reactions. Although complete structure of chloroplast FF has been reported, no high-resolution structure of an FF from photosynthetic bacteria has been available. Here, we report cryo-EM structures of an intact and functionally competent FF from (FF), a filamentous anoxygenic phototrophic bacterium from the earliest branch of photosynthetic organisms. The structures of FF in its ADP-free and ADP-bound forms for three rotational states reveal a previously unrecognized architecture of ATP synthases. A pair of peripheral stalks connect to the F head through a dimer of δ-subunits, and associate with two membrane-embedded a-subunits that are asymmetrically positioned outside and clamp F's c-ring. The two a-subunits constitute two proton inlets on the periplasmic side and two proton outlets on the cytoplasmic side, endowing FF with unique proton translocation pathways that allow more protons being translocated relative to single a-subunit FF. Our findings deepen understanding of the architecture and proton translocation mechanisms of FF synthases and suggest innovative strategies for modulating their activities by altering the number of a-subunit.
History
DepositionJul 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Mar 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
R: ATP synthase epsilon chain
S: ATP synthase subunit delta
Y: ATP synthase subunit b
V: ATP synthase subunit b
W: ATP synthase subunit delta
U: ATP synthase subunit b
X: ATP synthase subunit b
H: ATP synthase subunit c
I: ATP synthase subunit c
J: ATP synthase subunit c
K: ATP synthase subunit c
L: ATP synthase subunit c
M: ATP synthase subunit c
N: ATP synthase subunit c
O: ATP synthase subunit c
P: ATP synthase subunit c
Q: ATP synthase subunit c
T: ATP synthase subunit a
Z: ATP synthase subunit a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)628,54337
Polymers625,95126
Non-polymers2,59211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 8 types, 26 molecules ABCDEFGRSWYVUXHIJKLMNOPQTZ

#1: Protein ATP synthase subunit alpha / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 56563.340 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WGS6, H+-transporting two-sector ATPase
#2: Protein ATP synthase subunit beta / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 51755.691 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WGS4, H+-transporting two-sector ATPase
#3: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 32118.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WGS5
#4: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 15694.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WGS3
#5: Protein ATP synthase subunit delta / ATP synthase F(1) sector subunit delta / F-type ATPase subunit delta / F-ATPase subunit delta


Mass: 16552.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WGS7
#6: Protein
ATP synthase subunit b / ATP synthase F(0) sector subunit b / ATPase subunit I / F-type ATPase subunit b / F-ATPase subunit b


Mass: 18710.455 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WGS8
#7: Protein
ATP synthase subunit c / ATP synthase F(0) sector subunit c / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein


Mass: 7688.102 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WGS9
#8: Protein ATP synthase subunit a / ATP synthase F0 sector subunit a / F-ATPase subunit 6


Mass: 34176.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WGT0

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Non-polymers , 4 types, 11 molecules

#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#12: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ATP synthase / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85733 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00339976
ELECTRON MICROSCOPYf_angle_d0.55854331
ELECTRON MICROSCOPYf_dihedral_angle_d5.385809
ELECTRON MICROSCOPYf_chiral_restr0.0446439
ELECTRON MICROSCOPYf_plane_restr0.0057164

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