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- PDB-1ohh: BOVINE MITOCHONDRIAL F1-ATPASE complexed with the inhibitor prote... -

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Entry
Database: PDB / ID: 1ohh
TitleBOVINE MITOCHONDRIAL F1-ATPASE complexed with the inhibitor protein IF1
Components
  • (ATP synthase subunit ...) x 3
  • ATPase inhibitor, mitochondrial
KeywordsSYNTHASE / ATP PHOSPHORYLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP SYNTHASE / F1FO ATP SYNTHASE / F1-ATPASE
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 / negative regulation of hydrolase activity / ATPase inhibitor activity / heme biosynthetic process / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / negative regulation of hydrolase activity / ATPase inhibitor activity / 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 / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / erythrocyte differentiation / ADP binding / ATPase binding / protein homotetramerization / calmodulin binding / mitochondrial inner membrane / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
ATP synthase alpha/beta chain, C-terminal domain / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / 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 alpha/beta chain, C-terminal domain / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATPase inhibitor, 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 / MIR / Resolution: 2.8 Å
AuthorsCabezon, E. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: The Structure of Bovine F1-ATPase in Complex with its Regulatory Protein If1
Authors: Cabezon, E. / Montgomery, M.G. / Leslie, A.G.W. / 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.W. / 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: The Structure of Bovine If1, the Regulatory Subunit of Mitochondrial F-ATPase
Authors: Cabezon, E. / Runswick, M.J. / Leslie, A.G.W. / Walker, J.E.
History
DepositionMay 27, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2003Provider: repository / Type: Initial release
Revision 1.1Jun 2, 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 / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.status_code_sf / _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_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_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_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 17-STRANDED BARREL THIS IS REPRESENTED BY A 18-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

Downloads & links

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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: ATPase inhibitor, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,62018
Polymers360,9678
Non-polymers2,65310
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)272.300, 107.200, 152.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Number of models2

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Components

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ATP synthase subunit ... , 3 types, 7 molecules ABCDEFG

#1: Protein ATP synthase subunit alpha, mitochondrial


Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Tissue: MUSCLE / 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 (domestic cattle) / Organ: HEART / Tissue: MUSCLE
References: UniProt: P00829, H+-transporting two-sector ATPase
#3: Protein ATP synthase subunit gamma, mitochondrial / F-ATPase gamma subunit


Mass: 30185.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P05631

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Protein , 1 types, 1 molecules H

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


Mass: 9604.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: MUSCLE / Gene: ATPIF1, ATPI / Organ: HEART / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P01096

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Non-polymers , 2 types, 10 molecules

#5: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg

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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 REFERENCE STRUCTURE, (REFERENCE 1) THE BETA SUBUNITS WERE LABELED 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 BOUND AMPPNP) CONTRIBUTE TO THE CATALYTIC SITES OF THE BETA SUBUNITS, AND HAVE BEEN LABELED 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:. CHAIN A: ALPHA(E) CHAIN B: ALPHA(TP) CHAIN C: ALPHA(DP) CHAIN D: BETA(DP) CHAIN E: BETA(E) CHAIN F: BETA(TP)
Sequence detailsREFERENCE: 1) FOR THE ALPHA SUBUNIT: J. E. WALKER, S. J. POWELL, O. VINAS AND M. J. RUNSWICK, ...REFERENCE: 1) FOR THE ALPHA SUBUNIT: J. E. WALKER, S. J. POWELL, O. VINAS AND M. J. RUNSWICK, BIOCHEMISTRY VOL 28, PP 4702-4708, 1989. 2) FOR THE GAMMA SUBUNIT: M. R. DYER, N. J. GAY, S. J. POWELL AND J.E. WALKER, BIOCHEMISTRY VOL 28, PP 3670-3680, 1989. DIFFERENT RESIDUE: GLY A 481, GLY B 481, GLY C 481 THIS RESIDUE WAS IDENTIFIED AS A GLY FROM THE PROTEIN SEQUENCE. IN THE CDNA SEQUENCE, THE CODON FOR THIS RESIDUE WAS AGC (SER) IN THREE CLONES WHILE IN TWO OTHERS IT WAS GGC (GLY). THE DIFFERENCE WAS THOUGHT TO BE DUE TO A MUTATION OCCURRING DURING EITHER PROPAGATION OF THE CLONES IN THE LIBRARY OR SUBCLONING INTO M13 VECTORS. THE ELECTRON DENSITY SUGGESTS A GLY IN THIS POSITION. DIFFERENT RESIDUE: ASP G 273 THIS RESIDUE IS NOT PRESENT IN THE BOVINE GAMMA SUBUNIT IN THE MATERIAL USED IN THIS STRUCTURE DETERMINATION. THERE IS NO CODON FOR AN ASP IN THE CDNA SEQUENCE, NO C-TERMINAL ASP WAS FOUND IN THE PROTEIN SEQUENCE FOR THE GAMMA SUBUNIT AS ISOLATED FROM BEEF HEART MITOCHONDRIA.

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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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growpH: 6.6
Details: PROTEIN 20MG/ML IN 100MM PIPES-NAOH PH6.6, 40MM MGSO4, 0.04% NA AZIDE, 10% GLYCEROL, 0.002% PMSF. DROPS EQUAL VOLUME OF PROTEIN AND 10MM AMP-PNP, 300MM NACL, 16% PEG 4000, 5MM SPERMIDINE. BATCH METHOD., pH 6.60
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
210 mMAMP-PNP12
3300 mM12NaCl
416 %(w/v)PEG400012
55 mMspermidine12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9366
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9366 Å / Relative weight: 1
ReflectionResolution: 2.8→39.5 Å / Num. obs: 109367 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.03 % / Biso Wilson estimate: 82.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.1
Reflection shellResolution: 2.61→2.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 7.1 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 2.8 Å / % possible obs: 99.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 97.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 7.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1E1Q, BOVINE MITOCHONDRIAL F1-ATPASE

1e1q


Resolution: 2.8→39.5 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CRYSTALS ARE STATISTICALLY DISORDERED. IN THE ASYMMETRIC UNIT, THERE ARE TWO SUPERPOSED MOLECULES (COMPLEX A AND B) RELATED BY A 120 DEGREE ROTATION, EACH HAVE BEEN ASSIGNED AN OCCUPANCY OF ...Details: CRYSTALS ARE STATISTICALLY DISORDERED. IN THE ASYMMETRIC UNIT, THERE ARE TWO SUPERPOSED MOLECULES (COMPLEX A AND B) RELATED BY A 120 DEGREE ROTATION, EACH HAVE BEEN ASSIGNED AN OCCUPANCY OF 0.5 AND THEY ARE TREATED AS ALTERNATIVE CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 5507 5 %RANDOM
Rwork0.232 ---
obs0.232 109367 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.8 Å2 / ksol: 0.25 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.45 Å20 Å20 Å2
2--4.55 Å20 Å2
3----14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22699 0 160 0 22859
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.82
X-RAY DIFFRACTIONc_mcangle_it33
X-RAY DIFFRACTIONc_scbond_it4.24
X-RAY DIFFRACTIONc_scangle_it5.85
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.8→2.82 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.524 101 5 %
Rwork0.44 1944 -
Refinement
*PLUS
Rfactor Rfree: 0.277 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rwork: 0.44

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