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- PDB-1e79: Bovine F1-ATPase inhibited by DCCD (dicyclohexylcarbodiimide) -

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Entry
Database: PDB / ID: 1e79
TitleBovine F1-ATPase inhibited by DCCD (dicyclohexylcarbodiimide)
Components(ATP SYNTHASE ...) x 5
KeywordsHYDROLASE / ATP PHOSPHORYLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / F1FO ATP SYNTHASE / CENTRAL STALK
Function / homologyATP synthase, F1 complex, delta/epsilon subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase, F1 complex, gamma subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / AAA+ ATPase domain / ATP synthase, F1 complex, alpha subunit ...ATP synthase, F1 complex, delta/epsilon subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase, F1 complex, gamma subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / AAA+ ATPase domain / ATP synthase, F1 complex, alpha subunit / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, beta subunit / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / 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 / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / P-loop containing nucleoside triphosphate hydrolase / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / Mitochondrial ATP synthase epsilon chain / Cristae formation / Formation of ATP by chemiosmotic coupling / Mitochondrial protein import / 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 alpha/beta chain, C terminal domain / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase alpha/beta family, nucleotide-binding domain / ATP synthase / proton-transporting ATP synthase complex / negative regulation of cell adhesion involved in substrate-bound cell migration / angiostatin binding / 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 transmembrane transport / mitochondrial envelope / ATP biosynthetic process / proton transmembrane transporter activity / 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 / mitochondrial inner membrane / angiogenesis / response to oxidative stress / ATPase activity / myelin sheath / cell surface / ATP binding / plasma membrane / ATP synthase subunit beta, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit alpha, mitochondrial
Function and homology information
Specimen sourceBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.4 Å resolution
AuthorsGibbons, C. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: The Structure of the Central Stalk in Bovine F(1)-ATPase at 2.4 A Resolution.
Authors: Gibbons, C. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
#1: Journal: Science / Year: 1999
Title: Molecular Architecture of the Rotary Motor in ATP Synthase
Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E.
#2: Journal: Angew.Chem.Int.Ed.Engl. / Year: 1998
Title: ATP Synthesis by Rotary Catalysis (Nobel Lecture)
Authors: Walker, J.E.
#3: 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.
#4: 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.
#5: 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.
#6: Journal: J.Biol.Chem. / Year: 1981
Title: Inactivation of Bovine Mitochondrial F1-ATPase with Dicyclohexyl-Carbodiimide [14C] Leads to the Modification of a Specific Glutamic-Acid Residue in the Beta Subunit
Authors: Esch, F.S. / Bohlen, P. / Otsuka, A.S. / Yoshida, M. / Allison, W.S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 25, 2000 / Release: Nov 3, 2000
RevisionDateData content typeGroupProviderType
1.0Nov 3, 2000Structure modelrepositoryInitial release
1.1Aug 31, 2011Structure modelAtomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
1.2Nov 28, 2012Structure modelDatabase references
1.3Jan 22, 2014Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP SYNTHASE ALPHA CHAIN HEART ISOFORM
B: ATP SYNTHASE ALPHA CHAIN HEART ISOFORM
C: ATP SYNTHASE ALPHA CHAIN HEART ISOFORM
D: ATP SYNTHASE BETA CHAIN
E: ATP SYNTHASE BETA CHAIN
F: ATP SYNTHASE BETA CHAIN
G: ATP SYNTHASE GAMMA CHAIN
H: ATP SYNTHASE DELTA CHAIN
I: ATP SYNTHASE EPSILON CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,93022
Polyers372,1009
Non-polymers2,83013
Water16,412911
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)44050
ΔGint (kcal/M)-277.6
Surface area (Å2)114920
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)267.200, 107.200, 135.900
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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ATP SYNTHASE ... , 5 types, 9 molecules ABCDEFGHI

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


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 ATP SYNTHASE BETA CHAIN / BOVINE MITOCHONDRIAL F1-ATPASE


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 ATP SYNTHASE GAMMA CHAIN / BOVINE MITOCHONDRIAL F1-ATPASE


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
#4: Protein/peptide ATP SYNTHASE DELTA CHAIN / BOVINE MITOCHONDRIAL F1-ATPASE


Mass: 15074.813 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P05630, EC: 3.6.1.34
#5: Protein/peptide ATP SYNTHASE EPSILON CHAIN / BOVINE MITOCHONDRIAL F1-ATPASE


Mass: 5662.693 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P05632, EC: 3.6.1.34

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Non-polymers , 7 types, 924 molecules

#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Formula: Mg / Magnesium
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Formula: C3H8O3 / Glycerol
#10: Chemical ChemComp-DCW / DICYCLOHEXYLUREA


Mass: 224.342 Da / Num. of mol.: 1 / Formula: C13H24N2O / Dicyclohexylurea
#11: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4 / Sulfate
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 911 / 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 REFERENCE 4 , 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 CHAIN H: DELTA SUBUNIT CHAIN I: EPSILON SUBUNIT CRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN THE STRUCTURE. THE DCCD INHIBITION WAS CARRIED OUT IN THE PRESENCE OF ATP. THE DICYCLOHEXYL UREA IS THE MODIFIED FORM AND BINDS TO GLUTAMATE 199 IN SUBUNIT BETADP (CHAIN ID D)
Sequence detailsREFERENCE: 1) FOR THE ALPHA SUBUNIT: J. E. WALKER, S. J. POWELL, O. VINAS AND M. J. RUNSWICK, ...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: 2.61 / Density percent sol: 54 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 7.2 / Method: microdialysis
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
1100 mMTris-HCl1solution A
2200 mM1NaCl
34 mM1MgCl2
40.04 %(w/v)sodium azide1solution A
50.004 %(w/v)PMSF1solution B
614 %(w/v)PEG60001
70.660 mMADP1solution B
80.100 mMDCCD1solution B
95 mg/mlprotein1
12400 mM2NaCl
1310 mM2MgCl2
141 mMEDTA2
159 %(w/v)PEG60002
10solution A2half conc. of above
11solution B2

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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: ADSC CCD / Detector: CCD / Collection date: Jun 23, 1999
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: 36.405 / D resolution high: 2.4 / D resolution low: 2 / Number obs: 140093 / Observed criterion sigma I: 0 / Rmerge I obs: 0.088 / NetI over sigmaI: 8.1 / Redundancy: 2.4 % / Percent possible obs: 92.2
Reflection shellRmerge I obs: 0.331 / Highest resolution: 2.4 / Lowest resolution: 2.53 / MeanI over sigI obs: 2.1 / Redundancy: 1.8 % / Percent possible all: 68.6
Reflection shell
*PLUS
Percent possible obs: 68.6

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1E1Q, NATIVE FROZEN BOVINE MITOCHONDRIAL F1-ATPASE
Details: INITIAL REFINEMENT CARRIED OUT WITH REFMAC AND CNS UNRESOLVED SECTIONS ARE THE N-TERMINAL REGIONS OF THE ALPHA- AND BETA-SUBUNITS (RESIDUES 1-18 AND -4 - 8, RESPECTIVELY), THE C-TERMINAL REGIONS OF THE BETA-SUBUNITS (RESIDUES 475-478 IN TWO BETA-SUBUNITS AND 476-478 IN THE THIRD), TWO LOOP REGIONS IN THE GAMMA-SUBUNIT (RESIDUES 62-66 AND 97-100), RESIDUES 1-14 AND THE C-TERMINAL RESIDUE (146) OF THE DELTA-SUBUNIT, AND 3 RESIDUES (48-50) AT THE C-TERMINUS OF THE EPSILON-SUBUNIT. 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. REVDAT 2 INVOLVED RESIDUES 53-61 OF THE GAMMA SUBUNIT WHERE AN OUT-OF-REGISTER ERROR WAS CORRECTED
Overall SU B: 10.4 / Overall SU ML: 0.24 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.54 / Overall ESU R Free: 0.31
Displacement parametersB iso mean: 58.084
Least-squares processR factor R free: 0.281 / R factor R work: 0.225 / Highest resolution: 2.4 / Lowest resolution: 20 / Number reflection obs: 140093 / Percent reflection R free: 5 / Percent reflection obs: 92.2
Refine hist #LASTHighest resolution: 2.4 / Lowest resolution: 20
Number of atoms included #LASTProtein: 25232 / Nucleic acid: 0 / Ligand: 175 / Solvent: 911 / Total: 26318
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.020
X-RAY DIFFRACTIONp_angle_d0.0160.030
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0210.050
X-RAY DIFFRACTIONp_hb_or_metal_coord0.0440.055
X-RAY DIFFRACTIONp_mcbond_it1.03742.500
X-RAY DIFFRACTIONp_mcangle_it1.773.500
X-RAY DIFFRACTIONp_scbond_it2.625.000
X-RAY DIFFRACTIONp_scangle_it3.596.000
X-RAY DIFFRACTIONp_plane_restr0.0150.03
X-RAY DIFFRACTIONp_chiral_restr0.0900.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.300
X-RAY DIFFRACTIONp_multtor_nbd0.2080.300
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1690.300
X-RAY DIFFRACTIONp_planar_tor2.67.0
X-RAY DIFFRACTIONp_staggered_tor15.715.0
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.120.00
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Displacement parameters
*PLUS
B iso mean: 58.084
Least-squares process
*PLUS
R factor obs: 0.225

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