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- PDB-2w6h: Low resolution structures of bovine mitochondrial F1-ATPase durin... -

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Basic information

Entry
Database: PDB / ID: 2w6h
TitleLow resolution structures of bovine mitochondrial F1-ATPase during controlled dehydration: Hydration State 4A.
Components
  • ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM, MITOCHONDRIAL
  • ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
  • ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
  • ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
  • ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
KeywordsHYDROLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / TRANSIT PEPTIDE / F1FO ATP SYNTHASE / ATP PHOSPHORYLASE / ATP SYNTHASE / ION TRANSPORT / MITOCHONDRION / ATP SYNTHESIS / UBL CONJUGATION / CF(1) / P-LOOP / NUCLEOTIDE-BINDING / HYDROGEN ION TRANSPORT / PYRROLIDONE CARBOXYLIC ACID / ATP-BINDING
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / mitochondrial proton-transporting ATP synthase, catalytic core / proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / mitochondrial proton-transporting ATP synthase, catalytic core / proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / aerobic respiration / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
: / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / 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 ...: / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / 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, 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 / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / 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
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
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 Å
AuthorsSanchez-Weatherby, J. / Felisaz, F. / Gobbo, A. / Huet, J. / Ravelli, R.B.G. / Bowler, M.W. / Cipriani, F.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2009
Title: Improving diffraction by humidity control: a novel device compatible with X-ray beamlines.
Authors: Sanchez-Weatherby, J. / Bowler, M.W. / Huet, J. / Gobbo, A. / Felisaz, F. / Lavault, B. / Moya, R. / Kadlec, J. / Ravelli, R.B. / Cipriani, F.
History
DepositionDec 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.title
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM, MITOCHONDRIAL
B: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM, MITOCHONDRIAL
C: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM, 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


Theoretical massNumber of molelcules
Total (without water)404,9479
Polymers404,9479
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43360 Å2
ΔGint-220 kcal/mol
Surface area143010 Å2
MethodPQS
Unit cell
Length a, b, c (Å)107.900, 140.240, 268.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM, MITOCHONDRIAL / / F1-ATPASE ALPHA SUBUNIT


Mass: 59795.492 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle
References: UniProt: P19483, H+-transporting two-sector ATPase
#2: Protein ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL / / F1-ATPASE BETA SUBUNIT


Mass: 56340.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONRIA / Tissue: MUSCLESkeletal muscle
References: UniProt: P00829, H+-transporting two-sector ATPase
#3: Protein ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL / / F1-ATPASE GAMMA SUBUNIT


Mass: 33119.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONRIA / Tissue: MUSCLESkeletal muscle
References: UniProt: P05631, H+-transporting two-sector ATPase
#4: Protein ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL / / F1-ATPASE DELTA SUBUNIT


Mass: 17626.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONRIA / Tissue: MUSCLESkeletal muscle
References: UniProt: P05630, H+-transporting two-sector ATPase
#5: Protein ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL / / F1-ATPASE EPSILON SUBUNIT


Mass: 5793.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONRIA / Tissue: MUSCLESkeletal muscle
References: UniProt: P05632, H+-transporting two-sector ATPase

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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: 2.89 Å3/Da / Density % sol: 57.13 %
Description: THE DATA WERE COLLECTED AT ROOM TEMPERATURE, DURING CONTROLLED DEHYDRATION OF CRYSTALS,TO EVALUATE THE CHANGES THAT OCCUR IN CRYSTAL PACKING DURING DEHYDRATION. NO BIOLOGICAL ...Description: THE DATA WERE COLLECTED AT ROOM TEMPERATURE, DURING CONTROLLED DEHYDRATION OF CRYSTALS,TO EVALUATE THE CHANGES THAT OCCUR IN CRYSTAL PACKING DURING DEHYDRATION. NO BIOLOGICAL SIGNIFICANCE SHOULD BE ATTACHED TO THE COORDINATES.
Crystal growpH: 8.5
Details: 50 MM TRIS-HCL PH 8.2, 200 MM NACL, 20 MM MGSO4, 1 MM ADP, 1 MM ALCL3, 6 MM NAF 0.004% (W/V)PHENYLMETHYLSULFONYL FLUORIDE AND 12% (W/V) POLYETHYLENE GLYCOL 6000

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 16, 2008 / Details: GE211
RadiationMonochromator: DIAMOND111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 5→62 Å / Num. obs: 18314 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.3
Reflection shellResolution: 5→5.27 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0038refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMF

1bmf


Resolution: 5→62.14 Å / Cor.coef. Fo:Fc: 0.807 / SU B: 0.005 / SU ML: 0 / ESU R: 1.734 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA WERE COLLECTED AT ROOM TEMPERATURE, DURING CONTROLLED DEHYDRATION OF CRYSTALS,TO EVALUATE THE CHANGES THAT OCCUR IN CRYSTAL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA WERE COLLECTED AT ROOM TEMPERATURE, DURING CONTROLLED DEHYDRATION OF CRYSTALS,TO EVALUATE THE CHANGES THAT OCCUR IN CRYSTAL PACKING DURING DEHYDRATION. NO BIOLOGICAL SIGNIFICANCE SHOULD BE ATTACHED TO THE COORDINATES.
RfactorNum. reflection% reflection
Rwork0.296 --
obs0.296 18266 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---1.9 Å20 Å2
3---2.15 Å2
Refinement stepCycle: LAST / Resolution: 5→62.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25108 0 0 0 25108
LS refinement shellResolution: 5→5.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0 0
Rwork0.295 1303

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