[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


Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane ...Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
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, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta 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, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AUROVERTIN B / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic 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.
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
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38260 Å2
ΔGint-186 kcal/mol
Surface area102630 Å2
MethodPISA
Unit cell
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 (domestic 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 (domestic 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 (domestic 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


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


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


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
IDConc.Common 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

-
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
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0150.8
X-RAY DIFFRACTIONt_angle_deg2.511.6
X-RAY DIFFRACTIONt_dihedral_angle_d17.21
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0122
X-RAY DIFFRACTIONt_gen_planes0.0155
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.08215
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.285
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.21
X-RAY DIFFRACTIONt_planar_d0.0122
X-RAY DIFFRACTIONt_plane_restr0.0155

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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