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- PDB-9itz: Chloroflexus aurantiacus ADP-bound ATP synthase, state 3, focused... -

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Basic information

Entry
Database: PDB / ID: 9itz
TitleChloroflexus aurantiacus ADP-bound ATP synthase, state 3, focused refinement of FO
Components
  • ATP synthase subunit a
  • ATP synthase subunit b
  • ATP synthase subunit c
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 motive force-driven ATP synthesis / : / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane
Similarity search - Function
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, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily ...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, F0 complex, subunit C, bacterial/chloroplast / 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. / 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. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
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: 4.28 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: To Be Published
Title: An ATP synthase from the early photosynthetic prokaryote Chloroflexus aurantiacus has two proton-translocating a-subunits
Authors: Zhang, X. / Wu, J. / Xu, X.
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
Revision 1.0Mar 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: ATP synthase subunit b
X: ATP synthase subunit b
T: ATP synthase subunit a
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
V: ATP synthase subunit b
Y: ATP synthase subunit b
Z: ATP synthase subunit a


Theoretical massNumber of molelcules
Total (without water)220,07516
Polymers220,07516
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: 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
#2: 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
#3: 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
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: all / 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: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37529 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038233
ELECTRON MICROSCOPYf_angle_d0.58411288
ELECTRON MICROSCOPYf_dihedral_angle_d4.5231361
ELECTRON MICROSCOPYf_chiral_restr0.0451475
ELECTRON MICROSCOPYf_plane_restr0.0041508

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