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- PDB-5ari: Bovine mitochondrial ATP synthase state 2b -

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Basic information

Entry
Database: PDB / ID: 5ari
TitleBovine mitochondrial ATP synthase state 2b
Components
  • (ATP SYNTHASE F(0) COMPLEX SUBUNIT ...) x 2
  • (ATP SYNTHASE SUBUNIT ...) x 8
  • ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
KeywordsHYDROLASE / ATP SYNTHASE / ROTARY ATPASE
Function / homology
Function and homology information


Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / : / : / proton-transporting ATP synthase complex / : / : ...Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / : / : / proton-transporting ATP synthase complex / : / : / : / Mitochondrial protein degradation / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / aerobic respiration / proton transmembrane transport / ADP binding / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial ...ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / 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, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / 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
ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATP synthase-coupling factor 6, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase F(0) complex subunit C1, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsZhou, A. / Rohou, A. / Schep, D.G. / Bason, J.V. / Montgomery, M.G. / Walker, J.E. / Grigorieff, N. / Rubinstein, J.L.
CitationJournal: Elife / Year: 2015
Title: Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM.
Authors: Anna Zhou / Alexis Rohou / Daniel G Schep / John V Bason / Martin G Montgomery / John E Walker / Nikolaus Grigorieff / John L Rubinstein /
Abstract: Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic ...Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases.
History
DepositionSep 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
B: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
C: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
D: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
E: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
F: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
G: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
H: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
I: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
J: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
K: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
L: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
M: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
N: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
O: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
P: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
Q: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
S: ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL
T: ATP SYNTHASE F(0) COMPLEX SUBUNIT B1, MITOCHONDRIAL
U: ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL
V: ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
W: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)518,89322
Polymers518,89322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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ATP SYNTHASE SUBUNIT ... , 8 types, 12 molecules ABCDEFGHISUW

#1: Protein ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL


Mass: 55301.207 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 44-553 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: P19483
#2: Protein ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL


Mass: 51757.836 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 47-528 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA
References: UniProt: P00829, H+-transporting two-sector ATPase
#3: Protein ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL / F-ATPASE GAMMA SUBUNIT


Mass: 30300.760 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-298 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: P05631
#4: Protein ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL / F-ATPASE DELTA SUBUNIT


Mass: 15074.813 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 23-168 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: P05630
#5: Protein/peptide ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL / ATPASE SUBUNIT EPSILON


Mass: 5662.693 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-51 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: P05632
#7: Protein ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL / OLIGOMYCIN SENSITIVITY CONFERRAL PROTEIN / OSCP


Mass: 20989.803 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13621
#9: Protein ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL / ATPASE SUBUNIT D


Mass: 14167.169 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P13620
#11: Protein ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL


Mass: 23717.578 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 10-226 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: P00847

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ATP SYNTHASE F(0) COMPLEX SUBUNIT ... , 2 types, 9 molecules JKLMNOPQT

#6: Protein
ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL / ATP SYNTHASE LIPID-BINDING PROTEIN / ATP SYNTHASE PROTEOLIPID P1 / ATPASE PROTEIN 9 / ATPASE SUBUNIT C


Mass: 7293.593 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 63-134 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: P32876
#8: Protein ATP SYNTHASE F(0) COMPLEX SUBUNIT B1, MITOCHONDRIAL / ATP SYNTHASE SUBUNIT B / ATPASE SUBUNIT B


Mass: 20335.625 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 76-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P13619

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Protein , 1 types, 1 molecules V

#10: Protein ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL / ATPASE SUBUNIT F6


Mass: 9118.253 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 32-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P02721

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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: BOVINE MITOCHONDRIAL ATP SYNTHASE / Type: COMPLEX
Buffer solutionName: 20 MM TRIS-HCL, 100 MM NACL, 10% (V/V) DODECYLMALTOSIDE, 2 MM ATP, 0.02% (WT/V) NAN3
pH: 7.2
Details: 20 MM TRIS-HCL, 100 MM NACL, 10% (V/V) DODECYLMALTOSIDE, 2 MM ATP, 0.02% (WT/V) NAN3
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 27 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Mar 15, 2015
Details: K2 SUMMIT DIRECT DETECTOR DEVICE (GATAN INC.) OPERATED IN SUPER-RESOLUTION MODE WITH A 1.64 ANGSTROM PHYSICAL PIXEL AND 0. 82 ANGSTROM SUPER- RESOLUTION PIXEL. WITH NO SPECIMEN PRESENT, THE ...Details: K2 SUMMIT DIRECT DETECTOR DEVICE (GATAN INC.) OPERATED IN SUPER-RESOLUTION MODE WITH A 1.64 ANGSTROM PHYSICAL PIXEL AND 0. 82 ANGSTROM SUPER- RESOLUTION PIXEL. WITH NO SPECIMEN PRESENT, THE RATE OF EXPOSURE OF THE DETECTOR WAS 8 ELECTRONS PER PIXEL PER SECOND. EXPOSURE- FRACTIONATED MOVIES OF 20.1 S WERE RECORDED AS STACKS OF 67 FRAMES, SO THAT SELECTED SPECIMEN AREAS WERE EXPOSED WITH A TOTAL OF 60.3 ELECTRONS PER SQUARE ANGSTROM.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 18000 X / Calibrated magnification: 30487 X / Nominal defocus max: 4100 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderTemperature: 80 K
Image recordingElectron dose: 60.3 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)

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Processing

EM software
IDNameCategory
1MDFFmodel fitting
2UCSF Chimeramodel fitting
3FREALIGN3D reconstruction
4RELION3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING AND MAXIMUM LIKELIHOOD CLASSIFICATION
Resolution: 7.4 Å / Num. of particles: 17610
Details: THE A SUBUNIT WAS MODELED USING EVOLUTIONARY CO-VARIANCE. THE N-TERMINAL TRANSMEMBRANE HELICES OF THE B SUBUNIT WERE MODELED BASED ON TRANSMEMBRANE HELIX PREDICTIONS. SUBMISSION BASED ON ...Details: THE A SUBUNIT WAS MODELED USING EVOLUTIONARY CO-VARIANCE. THE N-TERMINAL TRANSMEMBRANE HELICES OF THE B SUBUNIT WERE MODELED BASED ON TRANSMEMBRANE HELIX PREDICTIONS. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3167. (DEPOSITION ID: 13799).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Details: METHOD--FLEXIBLE FITTING
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12WSS

2wss

12WSS1PDBexperimental model
22XND

2xnd

12XND2PDBexperimental model
32CLY

2cly

12CLY3PDBexperimental model
RefinementHighest resolution: 7.4 Å
Refinement stepCycle: LAST / Highest resolution: 7.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18545 0 0 0 18545

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