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- PDB-1bmf: BOVINE MITOCHONDRIAL F1-ATPASE -

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Basic information

Entry
Database: PDB / ID: 1bmf
TitleBOVINE MITOCHONDRIAL F1-ATPASE
Components(BOVINE MITOCHONDRIAL F1- ...) x 3
KeywordsATP PHOSPHORYLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP SYNTHASE / F1FO 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 / 2.85 Å resolution
AuthorsAbrahams, J.P. / Leslie, A.G.W. / Lutter, R. / Walker, J.E.
Citation
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.
#1: 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.
#2: 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: Mar 13, 1996 / Release: Dec 7, 1996
RevisionDateData content typeGroupProviderType
1.0Dec 7, 1996Structure modelrepositoryInitial release
1.1Mar 24, 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)353,93617
Polyers351,3637
Non-polymers2,57410
Water10,863603
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)37210
ΔGint (kcal/M)-194
Surface area (Å2)101480
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)284.220, 107.760, 139.680
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 / F1-ATPASE


Mass: 55301.207 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 / 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 / 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 , 4 types, 613 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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 PRIMARY REFERENCE, THE BETA SUBUNITS WERE LABELED 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 LABELED 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:. CHAIN A: ALPHA(E) CHAIN B: ALPHA(TP) CHAIN C: ALPHA(DP) CHAIN D: BETA(DP) CHAIN E: BETA(E) CHAIN F: BETA(TP) CHAIN G: GAMMA SUBUNIT
Nonpolymer detailsCRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN ...CRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN THE STRUCTURE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 17

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Sample preparation

CrystalDensity Matthews: 3.04 / Density percent sol: 54 %
Crystal growpH: 8.2 / Details: pH 8.2
Crystal grow
*PLUS
Temp: 22-24 ℃ / Method: microdialysis
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDDetails
150 mMTris-HCl11
29 %(w/v)PEG600011
3200 mMsodium chloride11*
41 mMEDTA11*
50.02 %(w/v)sodium azide11*
65 mM2-mercaptoethanol11
70.001 %PMSF11
85 mMdithiothreitol11*
920 mMmagnesium sulphate11
100.25 MAMP-PNP11*
110.005 MADP11*
128 mMmagnesium chloride12
1314 %(w/v)PEG600012
1412double the amount of *

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Data collection

DiffractionMean temperature: 269 kelvins
SourceSource: SYNCHROTRON / Type: SRS BEAMLINE PX9.6 / Synchrotron site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Sep 15, 1993
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionD resolution high: 2.85 Å / Number obs: 96689 / Observed criterion sigma I: 0 / Rmerge I obs: 0.098 / Redundancy: 5.4 % / Percent possible obs: 97.5
Reflection shellRmerge I obs: 0.19 / Highest resolution: 2.85 Å / Redundancy: 2.9 % / Percent possible all: 92
Reflection
*PLUS
D resolution high: 2.85 Å / Number all: 96689 / Percent possible obs: 97.5 / Rmerge I obs: 0.098 / Redundancy: 5.4 %
Reflection shell
*PLUS
Percent possible obs: 92 / Rmerge I obs: 0.19 / Redundancy: 2.9 %

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Processing

Software
NameVersionClassification
MULTIPLEISOMORPHOUS REPLACEMENTmodel building
PROLSQrefinement
MOSFLMdata reduction
CCP4data scaling
MULTIPLEISOMORPHOUS REPLACEMENTphasing
RefineStarting model: CCP4

Details: RESIDUES B 402 - B 409 INCLUSIVE HAVE BEEN GIVEN ZERO OCCUPANCY AS THERE WAS NO INTERPRETABLE ELECTRON DENSITY IN THIS REGION. 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) THE PEPTIDE BOND BETWEEN ASP 269 AND ASP 270 IN CHAINS A, B, C AND THE PEPTIDE BOND BETWEEN ASP 256 AND ASN 257 IN CHAINS D, E, AND F HAVE BEEN MODELED IN A CIS CONFORMATION. RESIDUAL FEATURES IN THE ELECTRON DENSITY MAP SUGGEST THAT THERE IS SOME CONFORMATIONAL DISORDER IN ASP 270 IN CHAINS A, B, AND C.
Sigma F: 0
Displacement parametersB iso mean: 41.6 Å2
Least-squares processHighest resolution: 2.85 Å / Lowest resolution: 6 Å / Number reflection obs: 86186 / Percent reflection obs: 95
Refine hist #LASTHighest resolution: 2.85 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 22722 / Nucleic acid: 0 / Ligand: 161 / Solvent: 603 / Total: 23486
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.020
X-RAY DIFFRACTIONp_angle_d0.0300.030
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.050
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.021.50
X-RAY DIFFRACTIONp_mcangle_it1.802.50
X-RAY DIFFRACTIONp_scbond_it2.162.50
X-RAY DIFFRACTIONp_scangle_it3.423.50
X-RAY DIFFRACTIONp_plane_restr0.0100.020
X-RAY DIFFRACTIONp_chiral_restr0.1350.150
X-RAY DIFFRACTIONp_singtor_nbd0.210.30
X-RAY DIFFRACTIONp_multtor_nbd0.240.30
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.210.30
X-RAY DIFFRACTIONp_planar_tor1.703.0
X-RAY DIFFRACTIONp_staggered_tor19.9215.00
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.3420.00
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refine
*PLUS
Sigma F: 0
Displacement parameters
*PLUS
B iso mean: 41.6 Å2
Least-squares process
*PLUS
R factor R free: 0.254 / R factor obs: 0.172 / Highest resolution: 2.85 Å / Lowest resolution: 6 Å / Number reflection obs: 86186 / Percent reflection R free: 5
Refine LS restraints
*PLUS
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.020
X-RAY DIFFRACTIONp_angle_d0.0300.030
X-RAY DIFFRACTIONp_planar_d0.0410.050
X-RAY DIFFRACTIONp_plane_restr0.0100.020
X-RAY DIFFRACTIONp_chiral_restr0.1350.150
X-RAY DIFFRACTIONp_mcbond_it1.021.50
X-RAY DIFFRACTIONp_scbond_it2.162.50
X-RAY DIFFRACTIONp_mcangle_it1.802.50
X-RAY DIFFRACTIONp_scangle_it3.423.50

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