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- PDB-1nbm: THE STRUCTURE OF BOVINE F1-ATPASE COVALENTLY INHIBITED WITH 4-CHL... -

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Basic information

Entry
Database: PDB / ID: 1nbm
TitleTHE STRUCTURE OF BOVINE F1-ATPASE COVALENTLY INHIBITED WITH 4-CHLORO-7-NITROBENZOFURAZAN
Components(F1-ATPASE) x 4
KeywordsATP SYNTHASE / F1FO ATP SYNTHASE / F1-ATPASE / 4-CHLORO-7-NITROBENZOFURAZAN / INHIBITION
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / 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 / ADP binding / mitochondrial inner membrane ...Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / 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 / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
ATP synthase alpha/beta chain, C-terminal domain / 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/beta chain, C-terminal domain / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / ATP synthase F(1) complex catalytic subunit beta, 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOrriss, G.L. / Leslie, A.G.W. / Braig, K. / Walker, J.E.
Citation
Journal: Structure / Year: 1998
Title: Bovine F1-ATPase covalently inhibited with 4-chloro-7-nitrobenzofurazan: the structure provides further support for a rotary catalytic mechanism.
Authors: Orriss, G.L. / Leslie, A.G. / Braig, K. / 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. / Lutter, R. / Walker, J.E.
History
DepositionApr 30, 1998Processing site: BNL
Revision 1.0Aug 26, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F1-ATPASE
B: F1-ATPASE
C: F1-ATPASE
D: F1-ATPASE
E: F1-ATPASE
F: F1-ATPASE
G: F1-ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,49518
Polymers350,8227
Non-polymers2,67211
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36930 Å2
ΔGint-211 kcal/mol
Surface area101300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)281.000, 106.600, 138.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 7 molecules ABCDFEG

#1: Protein F1-ATPASE / BOVINE MITOCHONDRIAL F1-ATPASE


Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P19483, EC: 3.6.1.34
#2: Protein F1-ATPASE / BOVINE MITOCHONDRIAL F1-ATPASE


Mass: 51532.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00829, EC: 3.6.1.34
#3: Protein F1-ATPASE / BOVINE MITOCHONDRIAL F1-ATPASE


Mass: 51667.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00829, EC: 3.6.1.34
#4: Protein F1-ATPASE / BOVINE MITOCHONDRIAL F1-ATPASE


Mass: 30185.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P05631, EC: 3.6.1.34

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Non-polymers , 5 types, 175 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: 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
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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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 PRIMARY REFERENCE, THE BETA SUBUNITS WERE LABELLED 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 BIND AMPPNP) CONTRIBUTE TO THE CATALYTIC SITES OF THE BETA SUBUNITS, AND HAVE BEEN LABELLED 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) CHAIN G IS THE GAMMA SUBUNIT.

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.5
Details: 50MM TRIS-HCL, PH7.5, 200MM SODIUM CHLORIDE, 20MM MAGNESIUM SULPHATE, 1MM EDTA, 0.002% (W/V) PHENYL METHYLSULPHONYL FLUORIDE, 0.02%(W/V) SODIUM AZIDE, 10.5% (W/V) PEG MME 5000, 250UM AMP-PNP AND 5UM ADP.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 7.2 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
2100 mMTris-HCl11
3400 mM11NaCl
44 mM11MgCl2
50.04 %(w/v)sodium azide11
60.004 %(w/v)phenylmethylsulphonyl fluoride11
712 %(w/v)PEG MME500011
82 mMAMP-PNP11
90.040 mMADP11
1050 mMTris-HCl12
11200 mM12NaCl
121 mMEDTA12
1320 mMmagnesium sulphate12
140.02 %(w/v)sodium azide12
150.002 %(w/v)phenylmethylsulphonyl fluoride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 70240 / % possible obs: 97.2 % / Redundancy: 2.5 % / Biso Wilson estimate: 54.48 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3.4 / % possible all: 98
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALUMINUM FLUORIDE INHIBITED FORM OF BOVINE MITOCHONDRIAL F1-ATPASE

Resolution: 3→6 Å / Isotropic thermal model: INDIVIDUAL / Cross valid method: FREE-R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.297 3434 2 %RANDOM
Rwork0.207 ---
obs0.207 66714 90.01 %-
Displacement parametersBiso mean: 52.67 Å2
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22732 0 161 164 23057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.994
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.17
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.95
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 3→3.12 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.367 316 2 %
Rwork0.293 6154 -
obs--89.23 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TYR.PARTYR.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.176
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.95

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