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- PDB-1qo1: Molecular Architecture of the Rotary Motor in ATP Synthase from Y... -

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Entry
Database: PDB / ID: 1qo1
TitleMolecular Architecture of the Rotary Motor in ATP Synthase from Yeast Mitochondria
Components
  • ATP SYNTHASE ALPHA CHAIN
  • ATP SYNTHASE BETA CHAIN
  • ATP SYNTHASE DELTA CHAIN
  • ATP SYNTHASE GAMMA CHAIN
  • ATP SYNTHASE PROTEIN 9
KeywordsATP SYNTHASE / LOW RESOLUTION MODEL / C-ALPHA ONLY
Function / homologyATP synthase, F1 complex, beta subunit / ATP synthase, F1 complex, alpha subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, F0 complex, subunit C / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, delta/epsilon subunit / V-ATPase proteolipid subunit C-like domain / AAA+ ATPase domain ...ATP synthase, F1 complex, beta subunit / ATP synthase, F1 complex, alpha subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, F0 complex, subunit C / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, delta/epsilon subunit / V-ATPase proteolipid subunit C-like domain / AAA+ ATPase domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATP synthase, F1 complex, gamma subunit conserved site / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / P-loop containing nucleoside triphosphate hydrolase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit superfamily / F0F1 ATP synthase delta/epsilon subunit, N-terminal / F/V-ATP synthase subunit C superfamily / ATP synthase / ATP synthase gamma subunit signature. / ATP synthase alpha and beta subunits signature. / ATP synthase alpha/beta family, beta-barrel domain / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / Mitochondrial protein import / ATP synthase alpha/beta chain, C terminal domain / ATP synthase subunit C / ATP synthase alpha/beta family, nucleotide-binding domain / F1F0 ATP synthase subunit C superfamily / Formation of ATP by chemiosmotic coupling / ATP synthase, alpha subunit, C-terminal domain superfamily / Cristae formation / ATP synthase c subunit signature. / angiostatin binding / negative regulation of cell adhesion involved in substrate-bound cell migration / mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) / mitochondrial proton-transporting ATP synthase complex / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase complex, coupling factor F(o) / ATP biosynthetic process / proton-transporting ATPase activity, rotational mechanism / ATP synthesis coupled proton transport / cellular response to interleukin-7 / H+-transporting two-sector ATPase / ATP hydrolysis coupled proton transport / mitochondrial nucleoid / electron transport chain / proton-transporting ATP synthase activity, rotational mechanism / MHC class I protein binding / ATP metabolic process / positive regulation of blood vessel endothelial cell migration / ADP binding / lipid metabolic process / regulation of intracellular pH / angiogenesis / response to oxidative stress / ATPase activity / lipid binding / cell surface / integral component of membrane / ATP binding / plasma membrane / ATP synthase subunit beta, mitochondrial / ATP synthase epsilon chain / ATP synthase subunit c / ATP synthase subunit gamma, mitochondrial / ATP synthase epsilon chain / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit c
Function and homology information
Specimen sourceSACCHAROMYCES CEREVISIAE (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.9 Å resolution
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, J, K, L, M, N, O, P, Q, R, S, T
AuthorsStock, D. / Leslie, A.G.W. / Walker, J.E.
Citation
Journal: Science / Year: 1999
Title: Molecular Architecture of the Rotary Motor in ATP Synthase
Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E.
#1: Journal: Biochemistry / Year: 1998
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: Journal: Structure / Year: 1997
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: Journal: Nature / Year: 1994
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 1, 1999 / Release: Nov 4, 1999

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP SYNTHASE ALPHA CHAIN
B: ATP SYNTHASE ALPHA CHAIN
C: ATP SYNTHASE ALPHA CHAIN
D: ATP SYNTHASE BETA CHAIN
E: ATP SYNTHASE BETA CHAIN
F: ATP SYNTHASE BETA CHAIN
G: ATP SYNTHASE GAMMA CHAIN
J: ATP SYNTHASE DELTA CHAIN
K: ATP SYNTHASE PROTEIN 9
L: ATP SYNTHASE PROTEIN 9
M: ATP SYNTHASE PROTEIN 9
N: ATP SYNTHASE PROTEIN 9
O: ATP SYNTHASE PROTEIN 9
P: ATP SYNTHASE PROTEIN 9
Q: ATP SYNTHASE PROTEIN 9
R: ATP SYNTHASE PROTEIN 9
S: ATP SYNTHASE PROTEIN 9
T: ATP SYNTHASE PROTEIN 9


Theoretical massNumber of molelcules
Total (without water)448,85118
Polyers448,85118
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)135.900, 175.300, 139.200
Angle α, β, γ (deg.)90.00, 91.60, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide ATP SYNTHASE ALPHA CHAIN / ATP1 / YBL099W / YBL0827 / Coordinate model: Cα atoms only


Mass: 55301.207 Da / Num. of mol.: 3
Details: THE BOS TAURUS (BOVINE) ATP SYNTHASE ALPHA CHAIN HEART ISOFORM SEQUENCE (SWISSPROT P19483) AND ...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) SACCHAROMYCES CEREVISIAE (baker's yeast) / Organelle: MITOCHONDRIALMitochondrion / References: UniProt: P19483, EC: 3.6.1.34
#2: Protein/peptide ATP SYNTHASE BETA CHAIN / ATP2 / YJR121W / J204 / Coordinate model: Cα atoms only


Mass: 51757.836 Da / Num. of mol.: 3
Details: THE BOS TAURUS (BOVINE) ATP SYNTHASE BETA CHAIN SEQUENCE (SWISSPROT P00829) AND MODEL (PDB ENTRY ...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) SACCHAROMYCES CEREVISIAE (baker's yeast) / Organelle: MITOCHONDRIALMitochondrion / References: UniProt: P00829, EC: 3.6.1.34
#3: Protein/peptide ATP SYNTHASE GAMMA CHAIN / ATP3 / YBR039W / YBR0408 / Coordinate model: Cα atoms only


Mass: 30185.674 Da / Num. of mol.: 1
Details: THE BOS TAURUS (BOVINE) ATP SYNTHASE GAMMA CHAIN SEQUENCE (SWISSPROT P05631) AND MODEL (PDB ENTRY ...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) SACCHAROMYCES CEREVISIAE (baker's yeast) / Organelle: MITOCHONDRIALMitochondrion / References: UniProt: P05631, EC: 3.6.1.34
#4: Protein/peptide ATP SYNTHASE DELTA CHAIN / ATP16 / YDL004W / YD8119.03 / D2935 / Coordinate model: Cα atoms only


Mass: 14897.904 Da / Num. of mol.: 1
Details: THE ESCHERICHIA COLI ATP SYNTHASE EPSILON CHAIN SEQUENCE (SWISSPROT P00832) AND MODEL (PDB ENTRY ...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) SACCHAROMYCES CEREVISIAE (baker's yeast) / Organelle: MITOCHONDRIALMitochondrion
References: UniProt: P00832, UniProt: P0A6E6*PLUS, EC: 3.6.1.34
#5: Protein/peptide
ATP SYNTHASE PROTEIN 9 / / LIPID-BINDING PROTEIN / ATP9 / OLI1 / PHO2 / Coordinate model: Cα atoms only


Mass: 8259.064 Da / Num. of mol.: 10
Details: THE ESCHERICHIA COLI ATP SYNTHASE C CHAIN SEQUENCE (SWISSPROT P00844) AND MODEL (PDB ENTRY 1A91) ...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) SACCHAROMYCES CEREVISIAE (baker's yeast) / Cellular location: MEMBRANEBiological membrane / Organelle: MITOCHONDRIALMitochondrion
References: UniProt: P00844, UniProt: P68699*PLUS, EC: 3.6.1.34
Compound detailsTHE F-TYPE ATPASES HAVE 2 COMPONENTS, F1 - THE CATALYTIC CORE AND F0 - THE MEMBRANE PROTON CHANNEL. ...THE F-TYPE ATPASES HAVE 2 COMPONENTS, F1 - THE CATALYTIC CORE AND F0 - THE MEMBRANE PROTON CHANNEL. F1 HAS FIVE SUBUNITS: ALPHA(3), BETA(3), GAMMA(1), DELTA(1), EPSILON(1). F0 HAS THREE MAIN SUBUNITS: A, B AND C. THE DBREF, SEQRES AND ATOM RECORDS GIVE THE BOVINE AND E.COLI MODEL COORDINATES AND SEQUENCE AS: THE TRUE YEAST PROTEINS ARE: WHILE THE MODELS USED ARE: CHAIN SWS-AC RESIDUES SWS-AC SEQUENCE PDB-1QO1 A P07251 36 545 P19483 67 553 24 510 B P07251 36 545 P19483 67 553 24 510 C P07251 36 545 P19483 62 553 19 510 D P00830 34 511 P00829 59 525 9 475 E P00830 34 511 P00829 59 524 9 474 F P00830 34 511 P00829 59 524 9 474 G P38077 34 311 P05631 26 297 1 272 CHAIN G FOUND IN 3 FRAGMENTS J Q12165 23 160 P00832 3 121 2 136 K P00841 1 76 P00844 1 79 1 79 L P00841 1 76 P00844 1 79 1 79 M P00841 1 76 P00844 1 79 1 79 N P00841 1 76 P00844 1 79 1 79 O P00841 1 76 P00844 1 79 1 79 P P00841 1 76 P00844 1 79 1 79 Q P00841 1 76 P00844 1 79 1 79 R P00841 1 76 P00844 1 79 1 79 S P00841 1 76 P00844 1 79 1 79 T P00841 1 76 P00844 1 79 1 79

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.66 / Density percent sol: 66 %
Crystal growpH: 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 grow
*PLUS
Temp: 4 ℃ / Method: batch method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
110 mg/mlprotein11
20.1 MTris11
312 %PEG600011
4150 mM11NaCl
51 mMAMP-PNP11
60.040 mMADP11
71 mMdithiothreitol11
80.02 %sodium azide11

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Feb 15, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionD resolution high: 3.9 Å / D resolution low: 15 Å / Number obs: 55593 / Rmerge I obs: 0.1 / NetI over sigmaI: 4 / Redundancy: 2.5 % / Percent possible obs: 93.3
Reflection shellRmerge I obs: 0.37 / Highest resolution: 3.9 Å / Lowest resolution: 4.11 Å / MeanI over sigI obs: 1.3 / Redundancy: 2.5 % / Percent possible all: 95.5
Reflection
*PLUS
Rmerge I obs: 0.1
Reflection shell
*PLUS
Number unique obs: 8288 / Percent possible obs: 95.5 / Rmerge I obs: 0.372

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BMF
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.
Least-squares processHighest resolution: 3.9 Å
Refine hist #LASTHighest resolution: 3.9 Å
Number of atoms included #LASTProtein: 3912 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3912
Least-squares process
*PLUS
R factor obs: 0.467 / Lowest resolution: 15 Å / Number reflection obs: 55593
Refine LS shell
*PLUS
R factor obs: 0.506

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