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- PDB-2w6i: Low resolution structures of bovine mitochondrial F1-ATPase durin... -

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Entry
Database: PDB / ID: 2w6i
TitleLow resolution structures of bovine mitochondrial F1-ATPase during controlled dehydration: Hydration State 4B.
Components
  • ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM, MITOCHONDRIAL
  • ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
  • ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
  • ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
  • F1-ATPASE DELTA SUBUNIT
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 / homologyAAA+ ATPase domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / F0F1 ATP synthase delta/epsilon subunit, N-terminal / 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 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, alpha subunit ...AAA+ ATPase domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / F0F1 ATP synthase delta/epsilon subunit, N-terminal / 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 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, alpha subunit / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta family, beta-barrel domain / Mitochondrial ATP synthase epsilon chain / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase alpha/beta family, nucleotide-binding domain / ATP synthase / Cristae formation / ATP synthase alpha/beta chain, C terminal domain / Formation of ATP by chemiosmotic coupling / Mitochondrial protein import / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase gamma subunit signature. / ATP synthase alpha and beta subunits signature. / 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 / ATP synthesis coupled proton transport / cellular response to interleukin-7 / H+-transporting two-sector ATPase / mitochondrial nucleoid / electron transport chain / 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 / 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 / 4 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 18, 2008 / Release: Oct 27, 2009
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 27, 2009Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jan 16, 2019Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.title
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. DETERMINATION METHOD: DSSP 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. DETERMINATION METHOD: DSSP 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. DETERMINATION METHOD: DSSP 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: F1-ATPASE DELTA SUBUNIT
I: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)404,9479
Polyers404,9479
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)40910
ΔGint (kcal/M)-201.4
Surface area (Å2)138470
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)108.920, 131.330, 267.380
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

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


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


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


Mass: 33119.035 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONRIA / Tissue: MUSCLE
References: UniProt: P05631, H+-transporting two-sector ATPase
#4: Protein/peptide F1-ATPASE DELTA SUBUNIT


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


Mass: 5793.889 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONRIA / Tissue: 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: 2.85 / Density percent sol: 50.05 %
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 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Details: GE211 / Detector: CCD / Collection date: Oct 30, 2008
RadiationMonochromator: DIAMOND111 / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionD resolution high: 4 Å / D resolution low: 101 Å / Number obs: 30825 / Observed criterion sigma I: 3 / Rmerge I obs: 0.22 / NetI over sigmaI: 14.3 / Redundancy: 2.5 % / Percent possible obs: 93.3
Reflection shellRmerge I obs: 0.6 / Highest resolution: 4 Å / Lowest resolution: 4.22 Å / MeanI over sigI obs: 1.7 / Redundancy: 2.4 % / Percent possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0038refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMF
Correlation coeff Fo to Fc: 0.815 / Correlation coeff Fo to Fc free: 0.808
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.
Overall SU B: 0.002 / Overall SU ML: 0 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 1.137 / Overall ESU R Free: 1.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 2 Å2 / Aniso B11: 2.09 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 1.58 Å2 / Aniso B23: 0 Å2 / Aniso B33: -3.67 Å2
Least-squares processR factor R free: 0.3 / R factor R work: 0.299 / R factor obs: 0.299 / Highest resolution: 4 Å / Lowest resolution: 3 Å / Number reflection R free: 1552 / Number reflection obs: 29141 / Percent reflection R free: 5.1 / Percent reflection obs: 92.8
Refine hist #LASTHighest resolution: 4 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 24216 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 24216
Refine LS shellHighest resolution: 4 Å / R factor R free: 0.325 / R factor R work: 0.35 / Lowest resolution: 4.1 Å / Number reflection R free: 104 / Number reflection R work: 2116 / Total number of bins used: 20

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