[English] 日本語
Yorodumi
- PDB-1cow: BOVINE MITOCHONDRIAL F1-ATPASE COMPLEXED WITH AUROVERTIN B -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) / mitochondrial proton-transporting ATP synthase complex / mitochondrial ATP synthesis coupled proton transport / ATP biosynthetic process / proton-transporting ATP synthase complex, catalytic core F(1) / ATP synthesis coupled proton transport / H+-transporting two-sector ATPase / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATPase activity ...mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) / mitochondrial proton-transporting ATP synthase complex / mitochondrial ATP synthesis coupled proton transport / ATP biosynthetic process / proton-transporting ATP synthase complex, catalytic core F(1) / ATP synthesis coupled proton transport / H+-transporting two-sector ATPase / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATPase activity / ATP binding / plasma membrane
ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase alpha/beta family, beta-barrel domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / P-loop containing nucleoside triphosphate hydrolase / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase, F1 complex, gamma subunit conserved site ...ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase alpha/beta family, beta-barrel domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / P-loop containing nucleoside triphosphate hydrolase / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / 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 alpha/beta chain, C terminal domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / ATP synthase, gamma subunit, helix hairpin domain / Elongation Factor Tu (Ef-tu); domain 3 / Thrombin, subunit H / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
ATP synthase subunit gamma, mitochondrial / ATP synthase subunit beta, mitochondrial / ATP synthase subunit alpha, mitochondrial
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
Authorsvan Raaij, M.J. / 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
History
DepositionMay 8, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 7, 2019Group: Data collection / Other / Structure summary / Category: audit_author / pdbx_database_status
Item: _audit_author.name / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Polymers351,3667
Non-polymers3,49512
Water9,332518
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38260 Å2
ΔGint-186 kcal/mol
Surface area102630 Å2
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-MP212121

-
Components

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

#1: Protein BOVINE MITOCHONDRIAL F1-ATPASE


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


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


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

-
Non-polymers , 5 types, 530 molecules

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


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


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-AUR / AUROVERTIN B


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


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O

-
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.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 54 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22-24 ℃ / pH: 7.2 / Method: microdialysis / Details: Lutter, R., (1993) J.Mol.Biol., 229, 787.
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDDetails
299.9 %deuterium oxide1
3100 mMTris-HCl1*
414 %(w/v)PEG60001
5400 mMsodium chloride1*
62 mMEDTA1*
70.04 %(w/v)sodium azide1*
80.02 %(w/v)PMSF1*
910 mMdithiothreitol1*
120 mMmagnesium sulphate2
108 mMmagnesium chloride1
110.500 mMAMP-PNP1*
120.010 mMADP1*
149 %(w/v)PEG60002
155 mM2-mercaptoethanol2
13* solutions2half of concentration * solutions

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 8, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 76643 / % possible obs: 97.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.075
Reflection
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 20 Å

-
Processing

Software
NameClassification
TNTrefinement
MOSFLMdata reduction
RefinementResolution: 3.1→20 Å /
RfactorNum. reflection
Rfree0.28 -
Obs-75180
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22722 0 222 518 23462
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealWeight
t_bond_d0.0150.8
t_angle_deg2.511.6
t_dihedral_angle_d17.21
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes0.0122
t_gen_planes0.0155
t_it
t_nbd0.08215
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.285
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealWeight
t_dihedral_angle_d
t_dihedral_angle_deg17.21
t_planar_d0.0122
t_plane_restr0.0155

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more