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- PDB-1qo1: Molecular Architecture of the Rotary Motor in ATP Synthase from Y... -
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Basic information
Entry | Database: PDB / ID: 1qo1 | ||||||
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Title | Molecular Architecture of the Rotary Motor in ATP Synthase from Yeast Mitochondria | ||||||
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![]() | ATP SYNTHASE / LOW RESOLUTION MODEL / C-ALPHA ONLY | ||||||
Function / homology | ![]() Formation of ATP by chemiosmotic coupling / Cristae formation / proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / : / : / Mitochondrial protein degradation / proton-transporting ATP synthase complex, coupling factor F(o) / : / proton motive force-driven ATP synthesis ...Formation of ATP by chemiosmotic coupling / Cristae formation / proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / : / : / 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-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 / ADP binding / membrane => GO:0016020 / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, J, K, L, M, N, O, P, Q, R, S, T | ||||||
![]() | Stock, D. / Leslie, A.G.W. / Walker, J.E. | ||||||
![]() | ![]() Title: Molecular Architecture of the Rotary Motor in ATP Synthase Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E. #1: ![]() Title: Solution Structure of the Transmembrane H -Transporting Subunit C of the F1F0 ATP Synthase Authors: Girvin, M.E. / Rastogi, V.K. / Abildgaard, F. / Markley, J.L. / Fillingame, R.H. #2: ![]() Title: Crystal Structure of the Epsilon Subunit of the Proton-Translocating ATP Synthase from Escherichia Coli Authors: Uhlin, U. / Cox, G.B. / Guss, J.M. #3: ![]() Title: Structure at 2.8-Angstrom Resolution of F1-ATPase from Bovine Heart Mitochondria Authors: Abrahams, J.P. / Leslie, A.G.W. / Lutter, R. / Walker, J.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.3 KB | Display | ![]() |
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PDB format | ![]() | 87.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 355.9 KB | Display | ![]() |
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Full document | ![]() | 356.2 KB | Display | |
Data in XML | ![]() | 1.1 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xokC ![]() 1bmfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: THE BOS TAURUS (BOVINE) ATP SYNTHASE ALPHA CHAIN HEART ISOFORM SEQUENCE (SWISSPROT P19483) AND MODEL (PDB ENTRY 1BMF) ARE GIVEN IN THE COORDINATES OF THIS ENTRY Source: (natural) ![]() ![]() #2: Protein | Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: THE BOS TAURUS (BOVINE) ATP SYNTHASE BETA CHAIN SEQUENCE (SWISSPROT P00829) AND MODEL (PDB ENTRY 1BMF) ARE GIVEN IN THE COORDINATES OF THIS ENTRY Source: (natural) ![]() ![]() #3: Protein | | Mass: 30185.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: THE BOS TAURUS (BOVINE) ATP SYNTHASE GAMMA CHAIN SEQUENCE (SWISSPROT P05631) AND MODEL (PDB ENTRY 1BMF) ARE GIVEN IN THE COORDINATES OF THIS ENTRY Source: (natural) ![]() ![]() #4: Protein | | Mass: 14897.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: THE ESCHERICHIA COLI ATP SYNTHASE EPSILON CHAIN SEQUENCE (SWISSPROT P00832) AND MODEL (PDB ENTRY 1AQT) ARE GIVEN IN THE COORDINATES OF THIS ENTRY Source: (natural) ![]() ![]() References: UniProt: P00832, UniProt: P0A6E6*PLUS, EC: 3.6.1.34 #5: Protein | Mass: 8259.064 Da / Num. of mol.: 10 / Source method: isolated from a natural source Details: THE ESCHERICHIA COLI ATP SYNTHASE C CHAIN SEQUENCE (SWISSPROT P00844) AND MODEL (PDB ENTRY 1A91) ARE GIVEN IN THE COORDINATES OF THIS ENTRY Source: (natural) ![]() ![]() References: UniProt: P00844, UniProt: P68699*PLUS, EC: 3.6.1.34 Compound details | THE F-TYPE ATPASES HAVE 2 COMPONENTS, F1 - THE CATALYTIC CORE AND F0 - THE MEMBRANE PROTON CHANNEL. ...THE F-TYPE ATPASES HAVE 2 COMPONENTS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: microbatch / pH: 8 Details: 0.1 M TRIS/CL PH8.0, 12% PEG 6000, 150 MM NACL, 1 MM AMP-PNP, 40 MICROM ADP, 1 MM DTT, 0.02% NAN3, MIXED 1:1 WITH PROTEIN SOLUTION UNDER PARAFFIN OIL IN MICROBATCH PLATE., pH 8.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→15 Å / Num. obs: 55593 / % possible obs: 93.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4 |
Reflection shell | Resolution: 3.9→4.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.3 / % possible all: 95.5 |
Reflection | *PLUS Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 95.5 % / Num. unique obs: 8288 / Rmerge(I) obs: 0.372 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BMF Highest resolution: 3.9 Å Details: THE MODEL CONSISTS OF C ALPHA COORDINATES OF PDB ENTRIES 1BMF, 1AQT, AND 1A91, WHICH WERE FITTED INTO THE DENSITY AS RIGID BODIES. NO REFINEMENT WAS CARRIED OUT ON THIS MODEL. THE ELECTRON ...Details: THE MODEL CONSISTS OF C ALPHA COORDINATES OF PDB ENTRIES 1BMF, 1AQT, AND 1A91, WHICH WERE FITTED INTO THE DENSITY AS RIGID BODIES. NO REFINEMENT WAS CARRIED OUT ON THIS MODEL. THE ELECTRON DENSITY AT 3.9 ANGSTROM RESOLUTION DOES NOT PROVIDE THE INFORMATION REQUIRED TO DERIVE AN ATOMIC MODEL. THE COORDINATES ARE BASED ON COORDINATES OF MODELS OF SUBUNITS OR DOMAINS DERIVED FROM HIGHER RESOLUTION X-RAY EXPERIMENTS (1BMF, 1AQT) OR NMR- EXPERIMENTS (1A91). THESE MODELS WERE FITTED INTO THE DENSITY AS RIGID BODIES. THEREFORE THE RESIDUE NAMES OF THE C ALPHA ATOMS HAVE NO MEANING. | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.9 Å
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Refinement | *PLUS Lowest resolution: 15 Å / Num. reflection obs: 55593 / Rfactor obs: 0.467 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.506 |