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- PDB-2f43: Rat liver F1-ATPase -

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Basic information

Entry
Database: PDB / ID: 2f43
TitleRat liver F1-ATPase
Components(ATP synthase ...) x 3
KeywordsHYDROLASE / ATP SYNTHASE / F0F1-ATPASE / OXIDATIVE PHOSPHORYLATION / MITOCHONDRIA / VANADATE
Function / homology
Function and homology information


lipoprotein particle receptor activity / Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / negative regulation of cell adhesion involved in substrate-bound cell migration / response to curcumin / response to 3,3',5-triiodo-L-thyronine / cold acclimation / cellular response to peptide ...lipoprotein particle receptor activity / Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / negative regulation of cell adhesion involved in substrate-bound cell migration / response to curcumin / response to 3,3',5-triiodo-L-thyronine / cold acclimation / cellular response to peptide / ATP biosynthetic process / angiostatin binding / COP9 signalosome / proton-transporting ATP synthase complex / cellular response to interleukin-7 / response to muscle activity / response to manganese ion / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / mitochondrial proton-transporting ATP synthase complex / negative regulation of endothelial cell proliferation / MHC class I protein binding / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / cellular response to nitric oxide / positive regulation of blood vessel endothelial cell migration / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton transmembrane transport / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / cellular response to dexamethasone stimulus / liver development / mitochondrial membrane / regulation of intracellular pH / ADP binding / lipid metabolic process / response to ethanol / angiogenesis / protease binding / mitochondrial inner membrane / membrane raft / calcium ion binding / cell surface / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / 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, 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 / Elongation Factor Tu (Ef-tu); domain 3 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / VANADATE ION / ATP synthase subunit beta, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit gamma, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChen, C. / Saxena, A.K. / Simcoke, W.N. / Garboczi, D.N. / Pedersen, P.L. / Ko, Y.H.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Mitochondrial ATP synthase: Crystal structure of the catalytic F1 unit in a vanadate-induced transition-like state and implications for mechanism.
Authors: Chen, C. / Saxena, A.K. / Simcoke, W.N. / Garboczi, D.N. / Pedersen, P.L. / Ko, Y.H.
#1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1998
Title: The 2.8-A structure of rat liver F1-ATPase: configuration of a critical intermediate in ATP synthesis/hydrolysis.
Authors: Bianchet, M.A. / Hullihen, J. / Pedersen, P.L. / Amzel, L.M.
#2: Journal: Biochim.Biophys.Acta / Year: 1994
Title: The three-dimensional structure of rat liver mitochodria F1-ATPase: X-ray diffraction studies.
Authors: Bianchet, M. / Medjahed, D. / Hulihen, J. / Pedersen, P.L. / Amzel, L.M.
#3: Journal: J.Bioenerg.Biomembr. / Year: 1992
Title: Quaternary structure of ATP synthases: symmetry and asymmetry in the F1 moiety.
Authors: Amzel, L.M. / Bianchet, M.A. / Pedersen, P.L.
#4: Journal: J.Biol.Chem. / Year: 1991
Title: Mitochondrial ATP synthase. Quaternary structure of the F1 moiety at 3.6 A determined by x-ray diffraction analysis.
Authors: Bianchet, M. / Ysern, X. / Hullihen, J. / Pedersen, P.L. / Amzel, L.M.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THIS PROTEIN HAS AN UNUSUAL STOICHIOMETRY AND THUS, UNUSUAL SYMMETRY. THE BIOLOGICAL UNIT (ACTIVE ENZYME) IS COMPOSED OF 3 A CHAINS, 3 B CHAINS AND 1 G CHAIN. IN THE R32 SPACEGROUP OF THIS CRYSTAL, THE ASYMMETRIC UNIT IS MADE UP OF ONE A CHAIN, ONE B CHAIN AND ONE-THIRD OF A G CHAIN. THE G CHAIN LIES ON THE 3-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS AND EACH ASYMMETRIC UNIT CONTAINS A RANDOM ONE OF THE THREE CRYSTALLOGRAPHICALLY SYMMETRIC POSITIONS. TO MAKE A BIOMOLECULE, THE 3-FOLD MATRICES IN REMARK 350 ARE ONLY APPLIED TO CHAIN A AND CHAIN B.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase alpha chain, mitochondrial
B: ATP synthase beta chain, mitochondrial
G: ATP synthase gamma chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,0688
Polymers136,9703
Non-polymers1,0985
Water0
1
A: ATP synthase alpha chain, mitochondrial
B: ATP synthase beta chain, mitochondrial
hetero molecules

A: ATP synthase alpha chain, mitochondrial
B: ATP synthase beta chain, mitochondrial
hetero molecules

A: ATP synthase alpha chain, mitochondrial
B: ATP synthase beta chain, mitochondrial
G: ATP synthase gamma chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,74122
Polymers350,4487
Non-polymers3,29415
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.567, 144.567, 362.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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ATP synthase ... , 3 types, 3 molecules ABG

#1: Protein ATP synthase alpha chain, mitochondrial


Mass: 55334.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER
References: UniProt: P15999, H+-transporting two-sector ATPase
#2: Protein ATP synthase beta chain, mitochondrial


Mass: 51404.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER
References: UniProt: P10719, H+-transporting two-sector ATPase
#3: Protein ATP synthase gamma chain, mitochondrial


Mass: 30231.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER
References: UniProt: P35435, H+-transporting two-sector ATPase

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Non-polymers , 4 types, 5 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 296 K / pH: 8.08
Details: 5MM ATP, 5MM MGCL2, 5MM VANADATE, 25MM NAN3, 50MM MOPS, pH 8.08, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99092
DetectorType: SBC-2 / Detector: CCD / Details: MONOCROMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99092 Å / Relative weight: 1
ReflectionResolution: 3→73.52 Å / Num. obs: 29647 / % possible obs: 100 % / Redundancy: 8.7 % / Rsym value: 0.143 / Net I/σ(I): 12.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.75 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MAB

1mab


Resolution: 3→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 7286337.69 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.32 1483 5 %RANDOM
Rwork0.306 ---
obs0.306 29509 99.9 %-
all-29509 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.4837 Å2 / ksol: 0.277358 e/Å3
Displacement parametersBiso mean: 67.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.3 Å23.32 Å20 Å2
2--7.3 Å20 Å2
3----14.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.78 Å
Refinement stepCycle: LAST / Resolution: 3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8169 0 65 0 8234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
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_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.11 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.377 144 5.2 %
Rwork0.405 2747 -
obs--100 %

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