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- PDB-4yxw: Bovine heart mitochondrial F1-ATPase inhibited by AMP-PNP and ADP... -

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Basic information

Entry
Database: PDB / ID: 4yxw
TitleBovine heart mitochondrial F1-ATPase inhibited by AMP-PNP and ADP in the presence of thiophosphate.
Components(ATP synthase subunit ...) x 5
KeywordsHYDROLASE / complex / mitochondrial
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / Mitochondrial protein degradation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / Mitochondrial protein degradation / proton transmembrane transporter activity / 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 / proton transmembrane transport / aerobic respiration / ADP binding / mitochondrial inner membrane / structural molecule activity / ATP hydrolysis activity / mitochondrion / 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 / Lysin / Thrombin, subunit H - #170 / : ...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 / Lysin / Thrombin, subunit H - #170 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / 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 / Pyruvate Kinase; Chain: A, domain 1 / 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, 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. / 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 / 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 / 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 / Monothiophosphate / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsBason, J.V. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: How release of phosphate from mammalian F1-ATPase generates a rotary substep.
Authors: Bason, J.V. / Montgomery, M.G. / Leslie, A.G. / Walker, J.E.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,04322
Polymers372,2189
Non-polymers2,82513
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45380 Å2
ΔGint-260 kcal/mol
Surface area111100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.353, 123.052, 261.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 55302.191 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: 30300.760 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
#4: Protein ATP synthase subunit delta, mitochondrial / F-ATPase delta subunit


Mass: 15074.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Heart / Tissue: Muscle / References: UniProt: P05630
#5: Protein/peptide ATP synthase subunit epsilon, mitochondrial / ATPase subunit epsilon


Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Heart / Tissue: Muscle / References: UniProt: P05632

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Non-polymers , 6 types, 50 molecules

#6: 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
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-TS6 / Monothiophosphate / phosphorothioic O,O,S-acid


Mass: 114.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3O3PS
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsSER 481 GLY in chains A, B and C was identified as a GLY from the protein sequence. In the cDNA ...SER 481 GLY in chains A, B and C 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.

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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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 295 K / Method: microdialysis / pH: 8.2
Details: PEG 6000, sodium chloride, magnesium chloride, Tris-HCl, AMP-PNP, ADP, sodium monothiophosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→76.52 Å / Num. obs: 59186 / % possible obs: 95.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 53.48 Å2 / CC1/2: 0.884 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.123 / Net I/σ(I): 6.4 / Num. measured all: 154361 / Scaling rejects: 36
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.7 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.1-3.180.6492.21164743600.5470.45996.1
13.86-76.520.09621.519137180.5960.07892.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLM7.1.0data reduction
Aimless0.1.29data scaling
PHASER2.52phasing
REFMAC5.8.0107refinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CK3

2ck3


Resolution: 3.1→76.5 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.883 / WRfactor Rfree: 0.2773 / WRfactor Rwork: 0.2283 / FOM work R set: 0.7774 / SU B: 28.758 / SU ML: 0.488 / SU Rfree: 0.5867 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2734 3000 5.1 %RANDOM
Rwork0.2263 ---
obs0.2287 55823 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 195.85 Å2 / Biso mean: 75.741 Å2 / Biso min: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å2-0 Å2-0 Å2
2---0.1 Å20 Å2
3---1.41 Å2
Refinement stepCycle: final / Resolution: 3.1→76.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24623 0 167 37 24827
Biso mean--55.71 47.45 -
Num. residues----3236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01925142
X-RAY DIFFRACTIONr_bond_other_d0.0010.0224860
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.98834081
X-RAY DIFFRACTIONr_angle_other_deg0.837357129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15853220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13324.21038
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.832154443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.14515182
X-RAY DIFFRACTIONr_chiral_restr0.0550.23976
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02128283
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025366
X-RAY DIFFRACTIONr_mcbond_it1.3767.59812928
X-RAY DIFFRACTIONr_mcbond_other1.3767.59712927
X-RAY DIFFRACTIONr_mcangle_it2.4611.38316142
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 223 -
Rwork0.317 4099 -
all-4322 -
obs--94.91 %

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