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- PDB-4xd7: Structure of thermophilic F1-ATPase inhibited by epsilon subunit -

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Basic information

Entry
Database: PDB / ID: 4xd7
TitleStructure of thermophilic F1-ATPase inhibited by epsilon subunit
Components(ATP synthase ...) x 4
KeywordsHYDROLASE / F1-ATPASE / ATP SYNTHASE / ROTARY MOTOR PROTEIN / ROTATIONAL CATALYSIS / BACILLUS PS3 / THERMOPHILIC
Function / homology
Function and homology information


: / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / 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 ...ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / 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 / Pyruvate Kinase; Chain: A, domain 1 / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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, 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 / 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
ADENOSINE-5'-DIPHOSPHATE / ATP synthase subunit beta / ATP synthase epsilon chain / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase subunit beta / ATP synthase epsilon chain
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.9 Å
AuthorsSHIRAKIHARA, Y. / SHIRATORI, A. / TANIKAWA, H. / NAKASAKO, M. / YOSHIDA, M. / SUZUKI, T.
CitationJournal: Febs J. / Year: 2015
Title: Structure of a thermophilic F1 -ATPase inhibited by an epsilon-subunit: deeper insight into the epsilon-inhibition mechanism.
Authors: Shirakihara, Y. / Shiratori, A. / Tanikawa, H. / Nakasako, M. / Yoshida, M. / Suzuki, T.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Source and taxonomy
Revision 1.2Apr 19, 2017Group: Structure summary
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
H: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,68513
Polymers374,8748
Non-polymers8115
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33470 Å2
ΔGint-243 kcal/mol
Surface area112850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.395, 233.395, 303.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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ATP synthase ... , 4 types, 8 molecules ABCDEFGH

#1: Protein ATP synthase subunit alpha / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 55317.543 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: atpA / Production host: Escherichia coli (E. coli)
References: UniProt: Q5KUJ1, UniProt: P09219*PLUS, H+-transporting two-sector ATPase
#2: Protein ATP synthase subunit beta / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 53949.949 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: atpD / Production host: Escherichia coli (E. coli)
References: UniProt: Q5KUJ3, UniProt: P07677*PLUS, H+-transporting two-sector ATPase
#3: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 32297.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: atpG / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KUJ2, UniProt: P09222*PLUS
#4: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14773.485 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: atpC / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KUJ4, UniProt: P07678*PLUS

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Non-polymers , 2 types, 5 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: 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

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Details

Has protein modificationY
Sequence detailsAuthor states that the sequence reported for this entry (Bacillus PS3 F1) matches better to that of ...Author states that the sequence reported for this entry (Bacillus PS3 F1) matches better to that of available UNP reference sequence for Geobacillus kaustophilus (strain HTA426) 235909, so Q5KUJ1, Q5KUJ2, Q5KUJ3 and Q5KUJ4 were selected as database reference sequence in this structure instead of UNP P09219 ,P07677,P09222 and P07678 which are outdated. The accession number at GenBank are LC076382 (Bacillus_PS3_alpha, Bacillus_PS3_gamma, Bacillus_PS3_beta) and LC076383 (Bacillus_PS3_ epsilon).

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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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: [drop]10 % PEG 6,000, 0.20 M sodium chloride, 0.05 M Tris-sulphate buffer (pH 8.0), 2mM DTT, 5mM CyDTA, 10% (v/v) ethyleneglycol and 10 mg/ml protein/ [reservoir] 14-16 % PEG 6,000, 0.2 M ...Details: [drop]10 % PEG 6,000, 0.20 M sodium chloride, 0.05 M Tris-sulphate buffer (pH 8.0), 2mM DTT, 5mM CyDTA, 10% (v/v) ethyleneglycol and 10 mg/ml protein/ [reservoir] 14-16 % PEG 6,000, 0.2 M sodium chloride, 0.05 M Tris-sulphate buffer (pH 8.0), 5mM CyDTA and 10% (v/v) ethyleneglycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97879 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 3.9→69.2 Å / Num. obs: 38420 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.7
Reflection shellResolution: 3.9→4.11 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.3 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementStarting model: 1SKY,1E79,1FS0

1sky

1e79

1fs0


Resolution: 3.9→19.989 Å / SU ML: 0.43 / σ(F): 1.9 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2817 3597 5.01 %
Rwork0.2498 --
obs0.2514 34904 98.96 %
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 88.442 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.1889 Å20 Å20 Å2
2--7.1889 Å2-0 Å2
3----12.8694 Å2
Refinement stepCycle: LAST / Resolution: 3.9→19.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22614 0 47 0 22661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01122949
X-RAY DIFFRACTIONf_angle_d1.50831013
X-RAY DIFFRACTIONf_dihedral_angle_d14.7728024
X-RAY DIFFRACTIONf_chiral_restr0.0983561
X-RAY DIFFRACTIONf_plane_restr0.0084117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-3.9510.31071510.30442589X-RAY DIFFRACTION96
3.951-4.00470.32561360.29822496X-RAY DIFFRACTION96
4.0047-4.06140.34811180.29512535X-RAY DIFFRACTION96
4.0614-4.12150.31121380.27742597X-RAY DIFFRACTION97
4.1215-4.18530.31851270.2792562X-RAY DIFFRACTION98
4.1853-4.25330.31171510.2772611X-RAY DIFFRACTION97
4.2533-4.32590.2761420.26162600X-RAY DIFFRACTION98
4.3259-4.40380.27681370.2562613X-RAY DIFFRACTION99
4.4038-4.48750.2881310.2492649X-RAY DIFFRACTION99
4.4875-4.57810.30351430.23662638X-RAY DIFFRACTION100
4.5781-4.67640.2591520.24492613X-RAY DIFFRACTION100
4.6764-4.78370.30271590.23942611X-RAY DIFFRACTION100
4.7837-4.90160.26281180.23922669X-RAY DIFFRACTION100
4.9016-5.03210.24011170.252654X-RAY DIFFRACTION100
5.0321-5.17770.29141800.25462638X-RAY DIFFRACTION100
5.1777-5.34170.32421020.27022686X-RAY DIFFRACTION100
5.3417-5.52880.30441580.2562607X-RAY DIFFRACTION100
5.5288-5.74510.27771310.25052684X-RAY DIFFRACTION100
5.7451-5.99980.31741270.26672653X-RAY DIFFRACTION100
5.9998-6.30670.34411390.27282651X-RAY DIFFRACTION100
6.3067-6.68790.28291250.27262656X-RAY DIFFRACTION100
6.6879-7.1820.30571290.23942658X-RAY DIFFRACTION100
7.182-7.86440.26571660.22382635X-RAY DIFFRACTION100
7.8644-8.9130.25281460.1882657X-RAY DIFFRACTION100
8.913-10.91610.20691350.19762633X-RAY DIFFRACTION100
10.9161-19.98880.2821390.29712657X-RAY DIFFRACTION99

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