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- PDB-1e1r: BOVINE MITOCHONDRIAL F1-ATPASE INHIBITED BY MG2+ADP AND ALUMINIUM... -

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Entry
Database: PDB / ID: 1e1r
TitleBOVINE MITOCHONDRIAL F1-ATPASE INHIBITED BY MG2+ADP AND ALUMINIUM FLUORIDE
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 / proton-transporting ATPase activity, rotational mechanism / cellular response to interleukin-7 / 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 / angiogenesis / response to oxidative stress / 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 / MOLECULAR REPLACEMENT / 2.5 Å resolution
AuthorsBraig, K. / Menz, R.I. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
Citation
Journal: Structure / Year: 2000
Title: Structure of Bovine Mitochondrial F1-ATPase Inhibited by Mg2+Adp and Aluminium Fluoride
Authors: Braig, K. / Menz, R.I. / Montgomery, M.G. / Leslie, A.G.W. / 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.W. / 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 10, 2000 / Release: Jun 28, 2000
RevisionDateData content typeGroupProviderType
1.0Jun 28, 2000Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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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)354,11519
Polyers351,3637
Non-polymers2,75212
Water15,493860
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)35690
ΔGint (kcal/M)-159.8
Surface area (Å2)126380
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)278.600, 106.700, 137.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21
DetailsTHE F1-ATPASE MOLECULE HAS THREE COPIES OF THENON-CATALYTIC ALPHA SUBUNIT AND THREE COPIES OF THECATALYTIC BETA SUBUNIT.IN THE PRIMARY REFERENCE, THE BETA SUBUNITS WERE LABELEDACCORDING TO THE BOUND NUCLEOTIDE, AS,BETA(DP) (BINDS ADP ),BETA(E) (NO BOUND NUCLEOTIDE) ANDBETA(TP) ( AMPPNP BOUND).THE ALPHA SUBUNITS (WHICH ALL BIND AMPPNP) CONTRIBUTE TOTHE CATALYTIC SITES OF THE BETA SUBUNITS, AND HAVE BEENLABELED ACCORDINGLY. THUS,ALPHA(DP) CONTRIBUTES TO THE CATALYTIC SITE ON BETA(DP),ALPHA(TP) TO THE SITE ON BETA ( TP) ANDALPHA(E) TO THE SITE ON BETA(E).THE CORRESPONDENCE BETWEEN THE SUBUNIT NAMES AND THE CHAINIDENTIFIERS 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

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Components

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

#1: Protein/peptide BOVINE MITOCHONDRIAL F1-ATPASE / ATP SYNTHASE ALPHA CHAIN HEART ISOFORM


Mass: 55301.207 Da / Num. of mol.: 3 / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P19483, EC: 3.6.1.34
#2: Protein/peptide BOVINE MITOCHONDRIAL F1-ATPASE / ATP SYNTHASE BETA CHAIN


Mass: 51757.836 Da / Num. of mol.: 3 / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00829, EC: 3.6.1.34
#3: Protein/peptide BOVINE MITOCHONDRIAL F1-ATPASE / ATP SYNTHASE GAMMA CHAIN


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

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Non-polymers , 6 types, 872 molecules

#4: 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
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Formula: Mg / Magnesium
#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-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Formula: AlF3 / Aluminium fluoride
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Formula: PO4 / Phosphate
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / Formula: H2O / Water

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Details

Sequence details1BMF A SWS P19483 1 - 66 NOT IN ATOMS LIST 1BMF B SWS P19483 1 - 66 NOT IN ATOMS LIST 1BMF C SWS ...1BMF A SWS P19483 1 - 66 NOT IN ATOMS LIST 1BMF B SWS P19483 1 - 66 NOT IN ATOMS LIST 1BMF C SWS P19483 1 - 61 NOT IN ATOMS LIST 1BMF D SWS P00829 1 - 58 NOT IN ATOMS LIST 1BMF D SWS P00829 526 - 528 NOT IN ATOMS LIST 1BMF E SWS P00829 1 - 58 NOT IN ATOMS LIST 1BMF E SWS P00829 525 - 528 NOT IN ATOMS LIST 1BMF F SWS P00829 1 - 58 NOT IN ATOMS LIST 1BMF F SWS P00829 525 - 528 NOT IN ATOMS LIST 1BMF G SWS P05631 1 - 25 NOT IN ATOMS LIST 1BMF G SWS P05631 298 - 298 NOT IN ATOMS LIST REFERENCE: 1) FOR THE ALPHA SUBUNIT: J. E. WALKER, S. J. POWELL, O. VINAS AND M. J. RUNSWICK, BIOCHEMISTRY VOL 28, PP 4702-4708, 1989. 2) FOR THE GAMMA SUBUNIT: M. R. DYER, N. J. GAY, S. J. POWELL AND J.E. WALKER, BIOCHEMISTRY VOL 28, PP 3670-3680, 1989. DIFFERENT RESIDUE: GLY A 481, GLY B 481, GLY C 481 THIS RESIDUE WAS IDENTIFIED AS A GLY FROM THE PROTEIN SEQUENCE. IN THE CDNA SEQUENCE, THE CODON FOR THIS RESIDUE WAS AGC (SER) IN THREE CLONES WHILE IN TWO OTHERS IT WAS GGC (GLY). THE DIFFERENCE WAS THOUGHT TO BE DUE TO A MUTATION OCCURRING DURING EITHER PROPAGATION OF THE CLONES IN THE LIBRARY OR SUBCLONING INTO M13 VECTORS. THE ELECTRON DENSITY SUGGESTS A GLY IN THIS POSITION. DIFFERENT RESIDUE: ASP G 273 THIS RESIDUE IS NOT PRESENT IN THE BOVINE GAMMA SUBUNIT IN THE MATERIAL USED IN THIS STRUCTURE DETERMINATION. THERE IS NO CODON FOR AN ASP IN THE CDNA SEQUENCE, NO C-TERMINAL ASP WAS FOUND IN THE PROTEIN SEQUENCE FOR THE GAMMA SUBUNIT AS ISOLATED FROM BEEF HEART MITOCHONDRIA.

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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: 2.92 / Density percent sol: 54 %
Description: 1BMF STRUCTURE WAS REFINED AGAINST DATA COLLECTED AT 277K, THIS DATA WAS COLLECTED AT 100K
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
pH: 8.2 / Method: microdialysis
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDDetails
199.9 %deuterium oxide11
2100 mMTris-HCl11
314 %(w/v)PEG600011
4400 mMsodium chloride11
52 mMEDTA11
60.04 %(w/v)sodium azide11
70.02 %(w/v)PMSF11
810 mMdithiothreitol11
98 mMmagnesium chloride11
100.5 mMAMP-PNP11
1110 mMADP11
1299.9 %deutrium oxide12
1350 mMTris-HCl12
149 %(w/v)PEG600012
15200 mMsodium chloride121 mM EDTA, 0.02%(w/v) sidium azide, 5mM 2-mercaptoethanol, 0.001% PMSF, 5mM dithiothreitol, 20mM magnesiumsulphate, 0.25mMAMP-PNP, 0.005mM ADP.

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Data collection

DiffractionMean temperature: 1
SourceSource: SYNCHROTRON / Type: SRS BEAMLINE PX9.6 / Synchrotron site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Feb 28, 1997
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 / Relative weight: 1
ReflectionB iso Wilson estimate: 32.8 / D resolution high: 2.48 / D resolution low: 2 / Number obs: 136913 / Observed criterion sigma I: 0 / Rmerge I obs: 0.096 / NetI over sigmaI: 7.5 / Redundancy: 2.34 % / Percent possible obs: 93.8
Reflection shellRmerge I obs: 0.282 / Highest resolution: 2.48 / Lowest resolution: 2.61 / MeanI over sigI obs: 2.8 / Redundancy: 2 % / Percent possible all: 74.6
Reflection
*PLUS
Number measured all: 320630
Reflection shell
*PLUS
Percent possible obs: 74.6

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1E1Q, BOVINE MITOCHONDRIAL F1-ATPASE AT 100K
Details: INITIAL REFINEMENT CARRIED OUT WITH TNT AND XPLOR 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. CRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN THE STRUCTURE.
Overall SU B: 10.7 / Overall SU ML: 0.24 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.46 / Overall ESU R Free: 0.31
Least-squares processR factor R free: 0.282 / R factor R work: 0.218 / Highest resolution: 2.5 / Lowest resolution: 20 / Number reflection R free: 6163 / Number reflection obs: 129652 / Percent reflection R free: 5 / Percent reflection obs: 95
Refine hist #LASTHighest resolution: 2.5 / Lowest resolution: 20
Number of atoms included #LASTProtein: 22663 / Nucleic acid: 0 / Ligand: 165 / Solvent: 860 / Total: 23688
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0100.020
X-RAY DIFFRACTIONp_angle_d0.0230.030
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.050
X-RAY DIFFRACTIONp_hb_or_metal_coord0.0680.050
X-RAY DIFFRACTIONp_mcbond_it1.72.5
X-RAY DIFFRACTIONp_mcangle_it2.63.5
X-RAY DIFFRACTIONp_scbond_it4.75.0
X-RAY DIFFRACTIONp_scangle_it6.06.0
X-RAY DIFFRACTIONp_plane_restr0.0190.020
X-RAY DIFFRACTIONp_chiral_restr0.110.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.30
X-RAY DIFFRACTIONp_multtor_nbd0.210.30
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.190.30
X-RAY DIFFRACTIONp_planar_tor3.17.0
X-RAY DIFFRACTIONp_staggered_tor16.515.00
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.520.00
X-RAY DIFFRACTIONp_special_tor

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