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- PDB-1mab: RAT LIVER F1-ATPASE -

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Basic information

Entry
Database: PDB / ID: 1mab
TitleRAT LIVER F1-ATPASE
Components(PROTEIN (F1-ATPASE ...) x 3
KeywordsHYDROLASE / ATP SYNTHASE / FOF1-ATPASE / OXIDATIVE PHOSPHORYLATION / MITOCHONDRIA
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 / cold acclimation / response to 3,3',5-triiodo-L-thyronine / 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 / cold acclimation / response to 3,3',5-triiodo-L-thyronine / cellular response to peptide / angiostatin binding / ATP biosynthetic process / COP9 signalosome / cellular response to interleukin-7 / response to manganese ion / response to muscle activity / proton-transporting ATP synthase complex / negative regulation of endothelial cell proliferation / MHC class I protein binding / proton motive force-driven ATP synthesis / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / positive regulation of blood vessel endothelial cell migration / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / cellular response to nitric oxide / proton transmembrane transport / receptor-mediated endocytosis / cellular response to dexamethasone stimulus / liver development / regulation of intracellular pH / mitochondrial membrane / ADP binding / lipid metabolic process / protease binding / angiogenesis / response to ethanol / 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, F1 complex, alpha subunit nucleotide-binding domain / 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. / 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 / 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 alpha, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.8 Å
AuthorsBianchet, M.A. / Amzel, L.M.
Citation
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.
#1: Journal: Biochim.Biophys.Acta / Year: 1994
Title: The Three-Dimensional Structure of Rat Liver Mitochondria F1-ATPase: X-Ray Diffraction Studies
Authors: Bianchet, M.A. / Medjahed, D. / Hullihen, J. / Pedersen, P.L. / Amzel, L.M.
#2: 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.
#3: Journal: J.Biol.Chem. / Year: 1991
Title: Quaternary Structure of ATP Synthases: Symmetry and Asymmetry in the F1 Moiety
Authors: Bianchet, M.A. / Ysernhullihen, J. / Pedersen, P.L. / Amzel, L.M.
History
DepositionAug 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 30, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4May 31, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (F1-ATPASE ALPHA CHAIN)
B: PROTEIN (F1-ATPASE BETA CHAIN)
G: PROTEIN (F1-ATPASE GAMMA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,7817
Polymers136,7273
Non-polymers1,0544
Water1,09961
1
A: PROTEIN (F1-ATPASE ALPHA CHAIN)
B: PROTEIN (F1-ATPASE BETA CHAIN)
hetero molecules

A: PROTEIN (F1-ATPASE ALPHA CHAIN)
B: PROTEIN (F1-ATPASE BETA CHAIN)
hetero molecules

A: PROTEIN (F1-ATPASE ALPHA CHAIN)
B: PROTEIN (F1-ATPASE BETA CHAIN)
G: PROTEIN (F1-ATPASE GAMMA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,39319
Polymers350,2327
Non-polymers3,16112
Water1267
TypeNameSymmetry operationNumber
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.670, 143.670, 361.150
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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PROTEIN (F1-ATPASE ... , 3 types, 3 molecules ABG

#1: Protein PROTEIN (F1-ATPASE ALPHA CHAIN)


Mass: 55348.219 Da / Num. of mol.: 1 / Fragment: ALPHA CHAIN / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER / References: UniProt: P15999, EC: 3.6.1.34
#2: Protein PROTEIN (F1-ATPASE BETA CHAIN)


Mass: 51404.461 Da / Num. of mol.: 1 / Fragment: BETA CHAIN / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER / References: UniProt: P10719, EC: 3.6.1.34
#3: Protein PROTEIN (F1-ATPASE GAMMA CHAIN)


Mass: 29974.396 Da / Num. of mol.: 1 / Fragment: GAMMA CHAIN / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER / References: UniProt: P35435, EC: 3.6.1.34

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Non-polymers , 5 types, 65 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.14
Details: 2.1 M AMMONIUM SULFATE AS PRECIPITANT, 0.2 M KPI (PH 7.14) BUFFER, 0.005 M ATP. AT ROOM TEMPERATURE
Temp details: room temp
Crystal grow
*PLUS
pH: 7.45 / Method: microdialysis / Details: Amzel, L.M., (1978) J.Biol.Chem., 253, 2067.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1200 mMpotassium phosphate11
25 mMATP11
315 mg/mlprotein11
4200 mMpotassium phosphate12
55 mMATP12
61 Mammonium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Details: MONOCROMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 35334 / % possible obs: 85.3 % / Redundancy: 11 % / Rsym value: 0.103 / Net I/σ(I): 7.1
Reflection
*PLUS
Rmerge(I) obs: 0.103
Reflection shell
*PLUS
Mean I/σ(I) obs: 7.1

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Processing

SoftwareName: X-PLOR / Version: 3.851 / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 2.8→6 Å / Cross valid method: THROUGHOUT / σ(F): 3
Details: FURTHER REFINEMENT IS IN PROGRESS. BECAUSE OF THE CRYSTAL SYMMETRY, THE INTERPRETABLE REGIONS OF THE GAMMA SUBUNIT ARE SEEN AS PARTIALLY OCCUPIED OVERLAPING COPIES. GAMMA AND SMALL REGIONS ...Details: FURTHER REFINEMENT IS IN PROGRESS. BECAUSE OF THE CRYSTAL SYMMETRY, THE INTERPRETABLE REGIONS OF THE GAMMA SUBUNIT ARE SEEN AS PARTIALLY OCCUPIED OVERLAPING COPIES. GAMMA AND SMALL REGIONS OF ALPHA AND BETA-SUBUNIT INTERACTING WITH GAMMA ARE REFINED WITH A PARTIAL OCUPPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29 -2.5 %RANDOM
Rwork0.217 ---
obs0.217 24960 65 %-
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8364 0 64 61 8489
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.08
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.73
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 6 Å / σ(F): 3 / % reflection Rfree: 2.5 % / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.73

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