[English] 日本語
Yorodumi
- PDB-6z1u: bovine ATP synthase F1c8-peripheral stalk domain, state 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z1u
Titlebovine ATP synthase F1c8-peripheral stalk domain, state 3
Components
  • (ATP synthase F(0) complex subunit ...) x 2
  • (ATP synthase subunit ...) x 6
  • ATP synthase-coupling factor 6, mitochondrial
  • ATPase inhibitor, mitochondrial
KeywordsHYDROLASE / ATP synthase / mitochondria / mammalian / complex
Function / homology
Function and homology information


negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / : / : ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / : / : / proton-transporting ATP synthase complex / heme biosynthetic process / : / : / : / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / aerobic respiration / proton transmembrane transport / erythrocyte differentiation / ADP binding / ATPase binding / protein homotetramerization / mitochondrial inner membrane / calmodulin binding / lipid binding / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B ...Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / 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, 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, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / 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. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsSpikes, T. / Montgomery, M.G. / Walker, J.E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105663150 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of the dimeric ATP synthase from bovine mitochondria.
Authors: Tobias E Spikes / Martin G Montgomery / John E Walker /
Abstract: The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial ...The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer-monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer-monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains.
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-11040
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11040
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP synthase subunit alpha, mitochondrial
B: ATP synthase subunit alpha, mitochondrial
C: ATP synthase subunit alpha, mitochondrial
D: ATP synthase subunit beta, mitochondrial
E: ATP synthase subunit beta, mitochondrial
F: ATP synthase subunit beta, mitochondrial
G: ATP synthase subunit gamma, mitochondrial
H: ATP synthase subunit delta, mitochondrial
I: ATP synthase subunit epsilon, mitochondrial
J: ATPase inhibitor, mitochondrial
K: ATP synthase F(0) complex subunit C2, mitochondrial
L: ATP synthase F(0) complex subunit C2, mitochondrial
M: ATP synthase F(0) complex subunit C2, mitochondrial
N: ATP synthase F(0) complex subunit C2, mitochondrial
P: ATP synthase F(0) complex subunit C2, mitochondrial
Q: ATP synthase F(0) complex subunit C2, mitochondrial
R: ATP synthase F(0) complex subunit C2, mitochondrial
S: ATP synthase subunit O, mitochondrial
b: ATP synthase F(0) complex subunit B1, mitochondrial
h: ATP synthase-coupling factor 6, mitochondrial
O: ATP synthase F(0) complex subunit C2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,46332
Polymers495,53821
Non-polymers2,92511
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
ATP synthase subunit ... , 6 types, 10 molecules ABCDEFGHIS

#1: Protein ATP synthase subunit alpha, mitochondrial / ATP synthase F1 subunit alpha


Mass: 55302.191 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: Chain ABC res 481: Residue 481 in chains A, B, and C in this structure should be GLY. There is no density to support a SER and negative density appears if you try SER. We have seen SER in ...Details: Chain ABC res 481: Residue 481 in chains A, B, and C in this structure should be GLY. There is no density to support a SER and negative density appears if you try SER. We have seen SER in some of our previous structures of bovine F1-ATPAse. We have used the following REMARK in other PDB files: REMARK 999 REFERENCE FOR THE ALPHA SUBUNIT J. E. WALKER, S. J. REMARK 999 POWELL,O. VINAS AND M. J. RUNSWICK, BIOCHEMISTRY,VOL 28,PP REMARK 999 4702-4708, 1989. REMARK 999 REMARK 999 SER 481 GLY IN CHAINS A, B AND C REMARK 999 WAS IDENTIFIED AS A GLY FROM THE PROTEIN REMARK 999 SEQUENCE. IN THE CDNA SEQUENCE, THE CODON FOR THIS REMARK 999 RESIDUE WAS AGC SER IN THREE CLONES WHILE IN TWO REMARK 999 OTHERS IT WAS GGC GLY. THE DIFFERENCE WAS THOUGHT TO REMARK 999 BE DUE TO A MUTATION OCCURRING DURING EITHER PROPAGATION REMARK 999 OF THE CLONES IN THE LIBRARY OR SUBCLONING INTO M13 REMARK 999 VECTORS. THE ELECTRON DENSITY SUGGESTS A GLY IN REMARK 999 THIS POSITION.
Source: (natural) Bos taurus (cattle) / References: UniProt: P19483
#2: Protein ATP synthase subunit beta, mitochondrial


Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: P00829, H+-transporting two-sector ATPase
#3: Protein ATP synthase subunit gamma, mitochondrial / F-ATPase gamma subunit


Mass: 30300.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P05631
#4: Protein ATP synthase subunit delta, mitochondrial / F-ATPase delta subunit


Mass: 15074.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P05630
#5: Protein/peptide ATP synthase subunit epsilon, mitochondrial / ATPase subunit epsilon


Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P05632
#8: Protein ATP synthase subunit O, mitochondrial / ATP synthase peripheral stalk subunit OSCP / Oligomycin sensitivity conferral protein / OSCP


Mass: 20959.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13621

-
Protein , 2 types, 2 molecules Jh

#6: Protein ATPase inhibitor, mitochondrial / Inhibitor of F(1)F(o)-ATPase / IF1


Mass: 7462.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ATP synthase inhibitor protein IF1 residues 1-60 with a 6HIS affinity tag
Source: (gene. exp.) Bos taurus (cattle) / Gene: ATPIF1, ATPI / Production host: Escherichia coli (E. coli) / References: UniProt: P01096
#10: Protein ATP synthase-coupling factor 6, mitochondrial / ATPase subunit F6 / ATP synthase peripheral stalk subunit F6


Mass: 8971.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02721

-
ATP synthase F(0) complex subunit ... , 2 types, 9 molecules KLMNPQROb

#7: Protein
ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 2 / ATP synthase ...ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 2 / ATP synthase proteolipid P2 / ATPase protein 9 / ATPase subunit c


Mass: 7653.034 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: Trimethyl-lysine at position 43 / Source: (natural) Bos taurus (cattle) / References: UniProt: P07926
#9: Protein ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase peripheral stalk-membrane subunit b / ATP synthase subunit b / ATPase subunit b


Mass: 24702.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13619

-
Non-polymers , 4 types, 28 molecules

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


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#12: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#13: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6HisCOMPLEX#1-#100MULTIPLE SOURCES
2ATP synthase F1 domainCOMPLEX#1-#51NATURALThe F1 domain of ATP synthase
3ATP synthase peripheral stalkCOMPLEX#7-#101NATURALPart of the stator of the enzyme
4ATPase inhibitor, mitochondrialCOMPLEX#61RECOMBINANTATPase inhibitor (truncated version of IF1)
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.487 MDaYES
210.372 MDaYES
310.0545 MDaYES
410.007441 MDa
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bos taurus (cattle)9913
23Bos taurus (cattle)9913
34Bos taurus (cattle)9913
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Nickel affinity purified filled by gel filtration
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 294 K
Details: The sample was allowed to penetrate through the holey support and to distribute to both sides of the grid surface for ca. 15 sec. Then the grids were blotted with filter paper for 8-10 sec before blotting.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 4.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refinedev_3885refinement
PHENIXdev_3885refinement
EM software
IDNameVersionCategory
4RELION3.1CTF correction
5CTFFIND4.1CTF correction
8Coot0.89model fitting
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14PHENIX1.17model refinement
15PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61458 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
12V7Q

2v7q

A1
22V7Q

2v7q

B1
32V7Q

2v7q

C1
42V7Q

2v7q

D1
52V7Q

2v7q

E1
62V7Q

2v7q

F1
72V7Q

2v7q

G1
82V7Q

2v7q

H1
92V7Q

2v7q

I1
102V7Q

2v7q

J1
112CLY

2cly

A1
122CLY

2cly

B1
132CLY

2cly

C1
142XND

2xnd

M1
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 53.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007532722
ELECTRON MICROSCOPYf_angle_d0.670244247
ELECTRON MICROSCOPYf_chiral_restr0.04545173
ELECTRON MICROSCOPYf_plane_restr0.00415666
ELECTRON MICROSCOPYf_dihedral_angle_d14.02364653

+
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