+
Open data
-
Basic information
Entry | Database: PDB / ID: 5fik | ||||||
---|---|---|---|---|---|---|---|
Title | Bovine mitochondrial ATP synthase state 3a | ||||||
![]() |
| ||||||
![]() | HYDROLASE / ATP SYNTHASE / ROTARY ATPASE | ||||||
Function / homology | ![]() 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 transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / aerobic respiration / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.4 Å | ||||||
![]() | Zhou, A. / Rohou, A. / Schep, D.G. / Bason, J.V. / Montgomery, M.G. / Walker, J.E. / Grigorieff, N. / Rubinstein, J.L. | ||||||
![]() | ![]() 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 |
| ||||||
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 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 "DA" 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. |
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 564.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 349.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3169MC ![]() 3164C ![]() 3165C ![]() 3166C ![]() 3167C ![]() 3168C ![]() 3170C ![]() 3181C ![]() 5araC ![]() 5areC ![]() 5arhC ![]() 5ariC ![]() 5fijC ![]() 5filC C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-ATP SYNTHASE SUBUNIT ... , 8 types, 12 molecules ABCDEFGHISUW
#1: Protein | Mass: 55301.207 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 44-553 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 51757.836 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 47-528 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P00829, H+-transporting two-sector ATPase #3: Protein | | Mass: 30300.760 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-298 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 15074.813 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 23-168 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein/peptide | | Mass: 5662.693 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-51 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | | Mass: 20989.803 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #9: Protein | | Mass: 14167.169 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-125 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #11: Protein | | Mass: 23717.578 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 10-226 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-ATP SYNTHASE F(0) COMPLEX SUBUNIT ... , 2 types, 9 molecules JKLMNOPQT
#6: Protein | Mass: 7293.593 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 63-134 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | | Mass: 20335.625 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 76-249 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Protein , 1 types, 1 molecules V
#10: Protein | Mass: 9118.253 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 32-108 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: BOVINE MITOCHONDRIAL ATP SYNTHASE / Type: COMPLEX |
---|---|
Buffer solution | Name: 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 |
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: 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, |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: 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 gun | Electron source: ![]() |
Electron lens | Mode: 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 holder | Temperature: 80 K |
Image recording | Electron dose: 60.3 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
-
Processing
EM software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: EACH PARTICLE | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Method: PROJECTION MATCHING AND MAXIMUM LIKELIHOOD CLASSIFICATION Resolution: 6.4 Å / Num. of particles: 24140 Details: THE A SUBUNIT WAS MODELLED USING EVOLUTIONARY CO-VARIANCE. THE N-TERMINAL TRANSMEMBRANE HELICES OF THE B SUBUNIT WERE MODELLED BASED ON TRANSMEMBRANE HELIX PREDICTIONS. SUBMISSION BASED ON ...Details: THE A SUBUNIT WAS MODELLED USING EVOLUTIONARY CO-VARIANCE. THE N-TERMINAL TRANSMEMBRANE HELICES OF THE B SUBUNIT WERE MODELLED BASED ON TRANSMEMBRANE HELIX PREDICTIONS. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3169. (DEPOSITION ID: 13801). Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Details: METHOD--FLEXIBLE FITTING | ||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||
Refinement | Highest resolution: 6.4 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6.4 Å
|