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- PDB-2w6e: Low resolution structures of bovine mitochondrial F1-ATPase durin... -

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Basic information

Entry
Database: PDB / ID: 2w6e
TitleLow resolution structures of bovine mitochondrial F1-ATPase during controlled dehydration:hydration state 1.
Components
  • ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM, MITOCHONDRIAL
  • ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
  • ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
KeywordsHYDROLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / TRANSIT PEPTIDE / F1FO ATP PHOSPHORYLASE / ION TRANSPORT / ATP SYNTHESIS / UBL CONJUGATION / CF(1) / P-LOOP / HYDROGEN ION TRANSPORT / PYRROLIDONE CARBOXYLIC ACID
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) ...Formation of ATP by chemiosmotic coupling / Cristae formation / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / 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 / ADP binding / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
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, 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 / 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 / ATP synthase subunit beta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.5 Å
AuthorsSanchez-Weatherby, J. / Felisaz, F. / Gobbo, A. / Huet, J. / Ravelli, R.B.G. / Bowler, M.W. / Cipriani, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Improving Diffraction by Humidity Control: A Novel Device Compatible with X-Ray Beamlines.
Authors: Sanchez-Weatherby, J. / Felisaz, F. / Gobbo, A. / Huet, J. / Ravelli, R.B.G. / Bowler, M.W. / 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-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 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)381,9538
Polymers381,5267
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31260 Å2
ΔGint-126.9 kcal/mol
Surface area103720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.490, 141.150, 285.280
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: MITOCHONDRIA / Tissue: 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: 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: MUSCLE
References: UniProt: P05631, H+-transporting two-sector ATPase
#4: 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

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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: 3.44 Å3/Da / Density % sol: 63.94 %
Description: DATA WERE COLLECTED AT ROOM TEMPERATURE DURING CONTROLLED DEHYDRATION OF THE CRYSTALS IN ORDER TO EVALUATE CHANGES IN CRYSTAL PACKING
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: Oct 29, 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: 6.5→60 Å / Num. obs: 8205 / % possible obs: 91.6 % / Observed criterion σ(I): 3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 10.5
Reflection shellResolution: 6.5→6.85 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.1 / % possible all: 92.1

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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: 6.5→30 Å / Cor.coef. Fo:Fc: 0.816 / Cor.coef. Fo:Fc free: 0.8 / SU B: 0.009 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 3.5 / ESU R Free: 3.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS STRUCTURE WAS DETERMINED TO EVALUATE CHANGING CRYSTAL CONTACTS DURING CONTROLLED DEHYDRATION OF CRYSTALS. NO BIOLOGICAL RELEVANCE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS STRUCTURE WAS DETERMINED TO EVALUATE CHANGING CRYSTAL CONTACTS DURING CONTROLLED DEHYDRATION OF CRYSTALS. NO BIOLOGICAL RELEVANCE SHOULD BE GIVEN TO THESE COORDINATES
RfactorNum. reflection% reflectionSelection details
Rfree0.285 373 4.8 %RANDOM
Rwork0.29 ---
obs0.289 7445 86.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1--3.04 Å20 Å20 Å2
2--1.49 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 6.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22663 0 27 0 22690
LS refinement shellResolution: 6.5→6.66 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.225 15
Rwork0.341 437

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