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- PDB-1cow: BOVINE MITOCHONDRIAL F1-ATPASE COMPLEXED WITH AUROVERTIN B -

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Entry
Database: PDB / ID: 1cow
TitleBOVINE MITOCHONDRIAL F1-ATPASE COMPLEXED WITH AUROVERTIN B
Components(BOVINE MITOCHONDRIAL F1- ...) x 3
KeywordsHYDROGEN ION TRANSPORT / ATP PHOSPHORYLASE / ATP SYNTHASE / F1F ATP SYNTHASE / F1-ATPASE
Function / homologyATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, beta subunit / ATP synthase, F1 complex, alpha subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / AAA+ ATPase domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit conserved site / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal ...ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, beta subunit / ATP synthase, F1 complex, alpha subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / AAA+ ATPase domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, gamma subunit / 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 subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase alpha/beta family, nucleotide-binding domain / ATP synthase / Cristae formation / Formation of ATP by chemiosmotic coupling / Mitochondrial protein import / ATP synthase gamma subunit signature. / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATP synthase alpha/beta family, beta-barrel domain / ATP synthase alpha/beta chain, C terminal domain / 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) / ATP biosynthetic process / cellular response to interleukin-7 / proton-transporting ATPase activity, rotational mechanism / ATP synthesis coupled proton transport / H+-transporting two-sector ATPase / electron transport chain / mitochondrial nucleoid / 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 / response to oxidative stress / angiogenesis / ATPase activity / myelin sheath / cell surface / ATP binding / plasma membrane / ATP synthase subunit beta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit alpha, mitochondrial
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 3.1 Å resolution
AuthorsVan Raaij, M. / Abrahams, J.P. / Leslie, A.G.W. / Walker, J.E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: The structure of bovine F1-ATPase complexed with the antibiotic inhibitor aurovertin B.
Authors: van Raaij, M.J. / Abrahams, J.P. / Leslie, A.G. / Walker, J.E.
#1: Journal: Nature / Year: 1994
Title: Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria
Authors: Abrahams, J.P. / Leslie, A.G. / Lutter, R. / Walker, J.E.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of F1-ATPase from Bovine Heart Mitochondria
Authors: Lutter, R. / Abrahams, J.P. / Van Raaij, M.J. / Todd, R.J. / Lundqvist, T. / Buchanan, S.K. / Leslie, A.G. / Walker, J.E.
#3: Journal: Embo J. / Year: 1993
Title: Inherent Asymmetry of the Structure of F1-ATPase from Bovine Heart Mitochondria at 6.5 A Resolution
Authors: Abrahams, J.P. / Lutter, R. / Todd, R.J. / Van Raaij, M.J. / Leslie, A.G. / Walker, J.E.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 8, 1996 / Release: Aug 17, 1996
RevisionDateData content typeGroupProviderType
1.0Aug 17, 1996Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BOVINE MITOCHONDRIAL F1-ATPASE
B: BOVINE MITOCHONDRIAL F1-ATPASE
C: BOVINE MITOCHONDRIAL F1-ATPASE
D: BOVINE MITOCHONDRIAL F1-ATPASE
E: BOVINE MITOCHONDRIAL F1-ATPASE
F: BOVINE MITOCHONDRIAL F1-ATPASE
G: BOVINE MITOCHONDRIAL F1-ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,86019
Polyers351,3667
Non-polymers3,49512
Water9,332518
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)38260
ΔGint (kcal/M)-186
Surface area (Å2)102630
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)283.400, 107.600, 140.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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BOVINE MITOCHONDRIAL F1- ... , 3 types, 7 molecules ABCDEFG

#1: Protein/peptide BOVINE MITOCHONDRIAL F1-ATPASE


Mass: 55302.191 Da / Num. of mol.: 3 / Source: (natural) Bos taurus (cattle) / Genus: Bos / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P19483, EC: 3.6.1.34
#2: Protein/peptide BOVINE MITOCHONDRIAL F1-ATPASE


Mass: 51757.836 Da / Num. of mol.: 3 / Source: (natural) Bos taurus (cattle) / Genus: Bos / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00829, EC: 3.6.1.34
#3: Protein/peptide BOVINE MITOCHONDRIAL F1-ATPASE


Mass: 30185.674 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / Genus: Bos / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P05631, EC: 3.6.1.34

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Non-polymers , 5 types, 530 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Formula: Mg / Magnesium
#5: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Formula: C10H17N6O12P3 / Comment: AMP-PNP (energy-carrying molecule analogue) *YM
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#7: Chemical ChemComp-AUR / AUROVERTIN B


Mass: 460.517 Da / Num. of mol.: 2 / Formula: C25H32O8
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Formula: H2O / Water

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Details

Compound detailsTHE F1-ATPASE MOLECULE HAS THREE COPIES OF THE NON-CATALYTIC ALPHA SUBUNIT AND THREE COPIES OF THE ...THE F1-ATPASE MOLECULE HAS THREE COPIES OF THE NON-CATALYTIC ALPHA SUBUNIT AND THREE COPIES OF THE CATALYTIC BETA SUBUNIT. IN THE FIRST REFERENCE (ABRAHAMS ET AL., 1994), THE BETA SUBUNITS WERE LABELLED ACCORDING TO THE BOUND NUCLEOTIDE, AS BETA(DP) (BINDS ADP), BETA(E) (NO BOUND NUCLEOTIDE) AND BETA(TP) (AMPPNP BOUND). THE ALPHA SUBUNITS (WHICH ALL BIND AMPPNP) CONTRIBUTE TO THE CATALYTIC SITES OF THE BETA SUBUNITS, AND HAVE BEEN LABELLED ACCORDINGLY. THUS ALPHA (DP) CONTRIBUTES TO THE CATALYTIC SITE ON BETA(DP), ALPHA (TP) TO THE SITE ON BETA(TP) AND ALPHA(E) TO THE SITE ON BETA(E). THE CORRESPONDENCE BETWEEN THE SUBUNIT NAMES AND THE CHAIN IDENTIFIERS IS GIVEN BELOW: THE POSITIONS OF SIDE CHAIN ATOMS WITH TEMPERATURE FACTORS GREATER THAN 75 IS UNCERTAIN. THE MAIN CHAIN CONFORMATION IS ALSO UNCERTAIN FOR REGIONS WITH TEMPERATURE FACTORS ABOVE 60. SOLVENT MOLECULES HAVE BEEN USED TO MODEL SOME FEATURES IN THE ELECTRON DENSITY THAT ARE PROBABLY DUE TO THE "MISSING" REGIONS OF THE GAMMA SUBUNIT (CHAIN G). OTHER SOLVENT MOLECULES (SOME WITH UNUSUALLY LOW B VALUES) MODEL OTHER FEATURES IN THE ELECTRON DENSITY WHICH PROBABLY REPRESENT LARGER MOLECULES (E.G. GLYCEROL) THAT COULD NOT BE IDENTIFIED UNAMBIGUOUSLY AT THE RESOLUTION OF THE ELECTRON DENSITY MAPS.
Sequence detailsRESIDUE NUMBERING: BY CONVENTION, THE FIFTH AMINO ACID (SERINE) IN THE BETA SUBUNITS (CHAINS D, E, ...RESIDUE NUMBERING: BY CONVENTION, THE FIFTH AMINO ACID (SERINE) IN THE BETA SUBUNITS (CHAINS D, E, F) IS RESIDUE 1 AND THE FIRST FOUR AMINO ACIDS ARE NUMBERED -4 TO -1.

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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: 3.04 / Density percent sol: 54 %
Crystal grow
*PLUS
Temp: 22-24 ℃ / pH: 7.2 / Method: microdialysis / Details: Lutter, R., (1993) J.Mol.Biol., 229, 787.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDDetails
299.9 %deuterium oxide11
3100 mMTris-HCl11*
414 %(w/v)PEG600011
5400 mMsodium chloride11*
62 mMEDTA11*
70.04 %(w/v)sodium azide11*
80.02 %(w/v)PMSF11*
910 mMdithiothreitol11*
120 mMmagnesium sulphate12
108 mMmagnesium chloride11
110.500 mMAMP-PNP11*
120.010 mMADP11*
149 %(w/v)PEG600012
155 mM2-mercaptoethanol12
13* solutions12half of concentration * solutions

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SRS BEAMLINE PX9.6 / Synchrotron site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Collection date: Aug 8, 1995
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNumber obs: 76643 / Rmerge I obs: 0.075 / Redundancy: 3 % / Percent possible obs: 97.6
Reflection
*PLUS
D resolution high: 3.1 Å / D resolution low: 2 Å

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Processing

Software
NameClassification
TNTrefinement
MOSFLMdata reduction
Least-squares processR factor R free: 0.28 / Highest resolution: 3.1 Å / Lowest resolution: 2 Å / Number reflection obs: 75180
Refine hist #LASTHighest resolution: 3.1 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 22722 / Nucleic acid: 0 / Ligand: 222 / Solvent: 518 / Total: 23462
Refine LS restraints
Refine IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0150.8
X-RAY DIFFRACTIONt_angle_deg2.511.6
X-RAY DIFFRACTIONt_dihedral_angle_d17.21.0
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0122.0
X-RAY DIFFRACTIONt_gen_planes0.0155.0
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.08215.0
Software
*PLUS
Name: TNT / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.285
Refine LS restraints
*PLUS
Refine IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.21.0
X-RAY DIFFRACTIONt_planar_d0.0122.0
X-RAY DIFFRACTIONt_plane_restr0.0155.0

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