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- PDB-2xnd: Crystal structure of bovine F1-c8 sub-complex of ATP Synthase -

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Basic information

Entry
Database: PDB / ID: 2xnd
TitleCrystal structure of bovine F1-c8 sub-complex of ATP Synthase
Components
  • (ATP SYNTHASE SUBUNIT ...) x 5
  • ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL
KeywordsHYDROLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP SYNTHESIS / F1FO ATP SYNTHASE / ION TRANSPORT / P-LOOP
Function / homology
Function and homology information


Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / mitochondrial proton-transporting ATP synthase, catalytic core / proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) ...Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / mitochondrial proton-transporting ATP synthase, catalytic core / proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / aerobic respiration / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / ATP synthase alpha/beta chain, C-terminal domain / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Lysin ...ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / ATP synthase alpha/beta chain, C-terminal domain / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Pyruvate Kinase; Chain: A, domain 1 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / 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 delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / 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 / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATP synthase subunit beta, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase F(0) complex subunit C1, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWatt, I.N. / Montgomery, M.G. / Runswick, M.J. / Leslie, A.G.W. / Walker, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Bioenergetic Cost of Making an Adenosine Triphosphate Molecule in Animal Mitochondria.
Authors: Watt, I.N. / Montgomery, M.G. / Runswick, M.J. / Leslie, A.G.W. / Walker, J.E.
History
DepositionAug 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references / Non-polymer description / Version format compliance
Revision 1.2Dec 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_sheet / 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 / _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_sheet.number_strands / _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 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-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 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
I: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
J: ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL
K: ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL
L: ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL
M: ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL
N: ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL
O: ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL
P: ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL
Q: ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,71629
Polymers418,87517
Non-polymers2,84112
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46460 Å2
ΔGint-259.8 kcal/mol
Surface area113200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.740, 157.100, 247.270
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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ATP SYNTHASE SUBUNIT ... , 5 types, 9 molecules ABCDEFGHI

#1: Protein ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL /


Mass: 53386.066 Da / Num. of mol.: 3 / Fragment: RESIDUES 62-553 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle
References: UniProt: P19483, H+-transporting two-sector ATPase
#2: Protein ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL /


Mass: 50365.371 Da / Num. of mol.: 3 / Fragment: RESIDUES 59-525 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal 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 / Fragment: RESIDUES 26-297 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle
References: UniProt: P05631, H+-transporting two-sector ATPase
#4: Protein ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL / / F-ATPASE DELTA SUBUNIT


Mass: 13811.496 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-167 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle
References: UniProt: P05630, H+-transporting two-sector ATPase
#5: Protein/peptide ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL / / ATPASE SUBUNIT EPSILON


Mass: 5275.220 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-48 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle
References: UniProt: P05632, H+-transporting two-sector ATPase

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Protein , 1 types, 8 molecules JKLMNOPQ

#6: Protein
ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL / ATP SYNTHASE PROTEOLIPID P1 / ATPASE PROTEIN 9 / ATPASE SUBUNIT C


Mass: 7293.593 Da / Num. of mol.: 8 / Fragment: RESIDUES 63-134 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle
References: UniProt: P32876, H+-transporting two-sector ATPase

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Non-polymers , 4 types, 12 molecules

#7: 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
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Details

Sequence detailsDIFFERENT RESIDUE: GLY A 481, GLY B 481, GLY C 481 THIS RESIDUE WAS IDENTIFIED AS A GLY FROM THE ...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 IN HIGHER RESOLUTION STRUCTURES SUGGESTS A GLY IN THIS POSITION.

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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: 3.17 Å3/Da / Density % sol: 61.16 % / Description: NONE
Crystal growpH: 7
Details: CRYSTALS WERE GROWN UNDER OIL BY MIXING EQUAL VOLUMES OF PROTEIN (10MG/ML IN 20MM TRIS PH 8.0, 10% GLYCEROL, 1MM ADP, 1MM AMP-PNP, 2MM MGSO4, 0.02% NAN3, 5.7MM TDM) AND PRECIPITANT SOLUTION ...Details: CRYSTALS WERE GROWN UNDER OIL BY MIXING EQUAL VOLUMES OF PROTEIN (10MG/ML IN 20MM TRIS PH 8.0, 10% GLYCEROL, 1MM ADP, 1MM AMP-PNP, 2MM MGSO4, 0.02% NAN3, 5.7MM TDM) AND PRECIPITANT SOLUTION (50MM HEPES PH 7.0, 14% PEG4600, 50MM K2HPO4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0007
DetectorType: MARRESEARCH / Detector: CCD / Date: May 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 3.5→132.6 Å / Num. obs: 72959 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 71.804 Å2 / Rmerge(I) obs: 0.26 / Net I/σ(I): 3.7
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E79

1e79


Resolution: 3.5→132.6 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.819 / SU B: 39.542 / SU ML: 0.602 / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.674 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.30397 3855 5 %RANDOM
Rwork0.26126 ---
obs0.26341 72959 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.15 Å2
Baniso -1Baniso -2Baniso -3
1--8.21 Å20 Å20 Å2
2--1.21 Å20 Å2
3---7 Å2
Refinement stepCycle: LAST / Resolution: 3.5→132.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28025 0 171 0 28196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02228570
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.98238717
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.63253873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97524.2921067
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.871154551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.08815182
X-RAY DIFFRACTIONr_chiral_restr0.0590.24560
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02121330
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2291.519185
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.419230223
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.31439385
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5624.58494
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 261 -
Rwork0.339 5330 -
obs--99.48 %

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