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- PDB-2qe7: Crystal structure of the f1-atpase from the thermoalkaliphilic ba... -

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Basic information

Entry
Database: PDB / ID: 2qe7
TitleCrystal structure of the f1-atpase from the thermoalkaliphilic bacterium bacillus sp. ta2.a1
Components
  • ATP synthase subunit alpha
  • ATP synthase subunit beta
  • ATP synthase subunit epsilon
  • ATP synthase subunit gamma
KeywordsHYDROLASE / blockage of ATP hydrolysis / F1-ATPase / ATP synthase / single particle analysis / thermoalkaliphilic
Function / homology
Function and homology information


thylakoid / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP binding / plasma membrane
Similarity search - Function
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 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 ...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 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, 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 / 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
ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsStocker, A. / Keis, S. / Vonck, J. / Cook, G.M. / Dimroth, P.
CitationJournal: Structure / Year: 2007
Title: The Structural Basis for Unidirectional Rotation of Thermoalkaliphilic F(1)-ATPase.
Authors: Stocker, A. / Keis, S. / Vonck, J. / Cook, G.M. / Dimroth, P.
History
DepositionJun 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 8, 2013Group: Refinement description
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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
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 subunit gamma
H: ATP synthase subunit epsilon


Theoretical massNumber of molelcules
Total (without water)362,7648
Polymers362,7648
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.210, 173.020, 218.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13D
23E
14D
24F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUPROPROAA27 - 50027 - 500
211GLUGLUPROPROBB27 - 50027 - 500
122GLUGLUPROPROAA27 - 50027 - 500
222GLUGLUPROPROCC27 - 50027 - 500
133ASNASNLEULEUDD2 - 4622 - 462
233ASNASNLEULEUEE2 - 4622 - 462
144ASNASNLEULEUDD2 - 4622 - 462
244ASNASNLEULEUFF2 - 4622 - 462

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.001785, -0.971851, 0.235591), (0.247257, -0.227848, -0.94178), (0.968948, 0.059933, 0.23989)0.495249, -13.4137, -8.6946
3given(-0.01717, 0.262378, 0.964812), (-0.970925, -0.234808, 0.046576), (0.238766, -0.935961, 0.258781)10.6763, -2.23016, -9.43767
4given(-0.021542, -0.972552, 0.231685), (0.267291, -0.228906, -0.936033), (0.963375, 0.041763, 0.264885)0.128083, -12.7281, -6.78129
5given(0.004944, 0.261873, 0.96509), (-0.966448, -0.246603, 0.071865), (0.256814, -0.933065, 0.251867)11.2511, -0.401973, -9.31946
DetailsThe biological assembly consists of one single TA2F1 molecule with alpha3-beta3-gamma-epsilon subunit stoichiometry. The alpha3-beta3 core complex possesses pseudo three-fold symmetry and the asymmetric part of the molecule represented by subunits gamma and epsilon exists in three alternate conformations.

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Components

#1: Protein ATP synthase subunit alpha


Mass: 55016.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: TA2.A1 / Gene: atpA / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): RNE41(DE3) / References: UniProt: Q71CG5, EC: 3.6.1.34
#2: Protein ATP synthase subunit beta


Mass: 50266.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: TA2.A1 / Gene: atpD / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): RNE41(DE3) / References: UniProt: Q71CG3, EC: 3.6.1.34
#3: Protein ATP synthase subunit gamma


Mass: 31932.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: TA2.A1 / Gene: atpG / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): RNE41(DE3) / References: UniProt: Q71CG4, EC: 3.6.1.34
#4: Protein ATP synthase subunit epsilon


Mass: 14983.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: TA2.A1 / Gene: atpC / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): RNE41(DE3) / References: UniProt: Q71CG2, EC: 3.6.1.34

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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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 8.8
Details: 1M LiCl, 0.1M Tris-HCl, 20% PEG 6000 , pH 8.8, MICRO-BATCH, temperature 296K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2005 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 3.06→50 Å / Num. obs: 90041 / % possible obs: 91.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 72.595 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 10.2
Reflection shellResolution: 3.06→3.25 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.716 / % possible all: 74.9

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMF

1bmf


Resolution: 3.06→39.997 Å / Isotropic thermal model: isotropic group / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.306 2094 2.5 %random
Rwork0.2519 ---
all-90041 --
obs-83712 94.61 %-
Solvent computationBsol: 137.521 Å2 / ksol: 0.271 e/Å3
Displacement parametersBiso mean: 77.22 Å2
Baniso -1Baniso -2Baniso -3
1-22.643 Å2-0 Å2-0 Å2
2---7.208 Å20 Å2
3----15.435 Å2
Refinement stepCycle: LAST / Resolution: 3.06→39.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24330 0 0 0 24330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_bond_d_na
X-RAY DIFFRACTIONf_bond_d_prot
X-RAY DIFFRACTIONf_angle_d0.662
X-RAY DIFFRACTIONf_angle_d_na
X-RAY DIFFRACTIONf_angle_d_prot
X-RAY DIFFRACTIONf_angle_deg
X-RAY DIFFRACTIONf_angle_deg_na
X-RAY DIFFRACTIONf_angle_deg_prot
X-RAY DIFFRACTIONf_dihedral_angle_d11.059
X-RAY DIFFRACTIONf_dihedral_angle_d_na
X-RAY DIFFRACTIONf_dihedral_angle_d_prot
X-RAY DIFFRACTIONf_improper_angle_d
X-RAY DIFFRACTIONf_improper_angle_d_na
X-RAY DIFFRACTIONf_improper_angle_d_prot
X-RAY DIFFRACTIONf_mcbond_it
X-RAY DIFFRACTIONf_mcangle_it
X-RAY DIFFRACTIONf_scbond_it
X-RAY DIFFRACTIONf_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsAuth asym-IDRefine-IDTypeRms dev position (Å)
11chain A & BAX-RAY DIFFRACTIONPOSITIONAL0.037
21chain A & CAX-RAY DIFFRACTIONB-FACTOR0.044
31chain D & EDX-RAY DIFFRACTIONPOSITIONAL0.046
41chain D & FDX-RAY DIFFRACTIONB-FACTOR0.037
LS refinement shellResolution: 3.06→3.1312 Å / Rfactor Rfree error: 0.062
RfactorNum. reflection% reflection
Rfree0.3993 137 -
Rwork0.3196 --
obs--93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0952-0.25410.14970.71350.02521.8918-0.21010.157-0.04060.09750.12180.0885-0.0868-0.25710.0560.23510.06470.11590.4274-0.05260.3313-43.044130.9149-21.8949
21.0123-0.19770.7250.61820.6223-0.50140.2582-0.25850.02020.3630.09080.11130.44890.0531-0.33810.90210.26040.06270.54940.01710.2743-23.91821.41275.568
32.8197-1.46420.7912.37110.0602-2.5739-1.1061-2.0398-0.07651.92710.98320.12350.7374-0.9088-0.00762.2620.5420.2631.7879-0.01320.4853-32.61225.800517.5828
40.9527-0.4038-0.10940.6388-0.09540.82810.0264-0.09020.1112-0.0941-0.0456-0.12260.04790.0530.03360.2017-0.05690.05390.2393-0.00240.3415-2.652433.024-57.3203
50.2009-1.01381.00482.2709-0.54780.7113-0.05830.1932-0.46030.35650.1889-0.5828-0.0460.083-0.04740.16070.0073-0.14220.33850.03180.552315.696617.8409-36.7699
6-3.74441.17641.31024.1019-1.82194.3669-0.24850.6228-0.42720.4948-0.5032-1.9062-0.42911.40440.74370.4796-0.2268-0.50821.4046-0.15811.367935.047724.561-38.3527
70.3079-0.43560.00830.8784-0.92811.4726-0.1620.0539-0.0715-0.07220.11460.17310.2501-0.18860.07970.3283-0.13760.07770.3499-0.08950.4919-34.1965-10.964-52.5764
83.0965-0.60081.96373.1397-0.158-0.18310.0116-0.61130.15190.53150.2788-0.05740.1063-0.569-0.25610.9964-0.03060.12711.12190.09070.6716-11.6918-25.449-21.0794
91.7855-0.56380.4705-0.95320.80961.594-0.1679-0.0044-0.31350.2055-0.15620.33190.7538-0.08570.35210.4340.01340.3670.10390.07160.6796-20.2111-39.9221-34.4549
10-0.81660.05330.59381.98560.0080.6165-0.4202-0.0150.3324-0.14090.44520.5420.044-0.857-0.030.268-0.22540.10520.76-0.16770.4791-57.247512.054-51.8438
11-0.4035-0.0244-0.08190.2877-0.181.10890.0191-0.02310.0955-0.07990.09940.3030.049-0.7137-0.0670.243-0.16860.1380.6133-0.07490.5012-54.9327-1.2415-28.0737
120.86711.6493-0.74111.1953-0.52130.8216-0.1008-0.2043-0.75930.03860.0015-0.4542-0.13790.17680.30170.253-0.08660.13110.5998-0.13020.5575-43.65969.2288-31.0282
131.13590.52350.6569-0.2928-0.16340.69950.1403-0.216-0.33810.228-0.16310.03940.0959-0.1148-0.00360.7274-0.16970.1850.4520.08910.5016-37.8393-7.5708-3.2966
141.0002-0.26840.7779-0.02230.17551.3678-0.0075-0.17580.1808-0.1162-0.0576-0.0071-0.404-0.32950.13630.18260.0597-0.06980.2026-0.02430.3373-29.0151.7314-42.4981
150.9559-0.27090.86420.1084-0.34671.471-0.1654-0.10130.0255-0.0167-0.0751-0.2345-0.2499-0.16060.22070.18360.04160.00680.1796-0.04830.3172-13.569346.5921-25.8628
160.8676-1.03-0.4239-1.0760.28582.36060.1862-0.07160.32040.0535-0.1098-0.03790.45610.3364-0.25210.15760.079-0.04910.1109-0.09660.3351-14.829636.7448-37.1526
172.469-0.02661.61830.5767-0.5031.44010.2296-0.0929-0.40530.0321-0.0991-0.3070.0744-0.1019-0.13160.2627-0.0551-0.07880.205-0.04770.36945.633535.9092-12.6105
180.7928-0.7080.29111.5322-0.55131.0940.05070.0594-0.0393-0.6762-0.1032-0.08250.4775-0.09320.00760.4763-0.06490.09940.239-0.0990.3089-13.43687.0831-72.2745
191.3877-0.19130.111-0.1222-0.59350.82-0.13690.04820.2517-0.16880.0237-0.09980.1791-0.06650.09530.2413-0.04640.14670.1673-0.06990.2781-0.68210.3486-67.5873
201.1929-0.0847-0.65370.7538-0.53440.6228-0.1199-0.1403-0.0578-0.08570.06760.18120.09890.0891-0.02990.5103-0.0010.16730.3252-0.02430.3845-14.70332.9258-57.0975
210.975-1.0223-0.58661.24350.65530.7589-0.4043-0.2492-0.06360.29330.1020.25170.4040.17190.0470.41520.30130.28570.26370.07950.29799.4821-17.5207-46.0221
220.00740.0166-0.00980.00260.0159-0.0248-0.0204-0.0955-0.03380.116-0.04040.1037-0.0276-0.043-0.5591-0.2435-0.12290.2064-0.14650.1517-0.18190.4408-2.0647-10.7983
232.0144-0.5771-0.9130.2550.11280.71820.1777-0.3266-0.0454-0.1911-0.0914-0.06420.25050.18480.7899-0.56320.27070.4384-0.11160.1448-0.022517.6849-11.844910.2186
240.2773-0.19910.28270.4058-0.47870.70720.0967-0.03240.022-0.1509-0.1383-0.090.0101-0.13590.0626-0.27130.0990.16320.02610.10750.12336.7712-5.8947-2.8735
25-0.91510.2233-0.5131-0.469-0.2345-0.7072-0.0417-0.4387-0.12680.2705-0.4557-0.299-0.54760.84330.48430.9173-0.5184-0.44361.26920.48061.00724.3046-14.368514.4629
260.43310.4725-0.99230.50290.8595-0.01690.1642-0.3122-0.0310.58060.1925-0.06110.05610.3211-0.05360.54990.32320.04491.02360.63860.411128.3254-15.96218.9821
270.0964-0.15880.04430.18490.84811.29660.048-0.232-0.01720.2265-0.0098-0.25780.31070.3876-0.09730.5660.0133-0.25430.24230.24910.294622.404-13.306313.3544
280.21850.0626-0.12320.50960.25730.13450.0056-0.5421-0.18890.3391-0.22870.0961-0.30270.0662-0.05111.1482-0.5673-0.17691.01030.08190.430323.237-11.985514.8571
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 3641 - 338
2X-RAY DIFFRACTION2AA365 - 443339 - 417
3X-RAY DIFFRACTION3AA444 - 500418 - 474
4X-RAY DIFFRACTION4BB27 - 3211 - 295
5X-RAY DIFFRACTION5BB322 - 441296 - 415
6X-RAY DIFFRACTION6BB442 - 500416 - 474
7X-RAY DIFFRACTION7CC27 - 3801 - 354
8X-RAY DIFFRACTION8CC381 - 415355 - 389
9X-RAY DIFFRACTION9CC416 - 500399 - 474
10X-RAY DIFFRACTION10DD2 - 581 - 57
11X-RAY DIFFRACTION11DD59 - 24858 - 247
12X-RAY DIFFRACTION12DD249 - 309248 - 308
13X-RAY DIFFRACTION13DD310 - 462309 - 461
14X-RAY DIFFRACTION14EE2 - 1241 - 123
15X-RAY DIFFRACTION15EE125 - 259124 - 258
16X-RAY DIFFRACTION16EE260 - 310259 - 309
17X-RAY DIFFRACTION17EE311 - 462310 - 461
18X-RAY DIFFRACTION18FF2 - 1581 - 157
19X-RAY DIFFRACTION19FF159 - 245158 - 244
20X-RAY DIFFRACTION20FF246 - 318245 - 317
21X-RAY DIFFRACTION21FF319 - 462318 - 461
22X-RAY DIFFRACTION22GG3 - 393 - 39
23X-RAY DIFFRACTION23GG40 - 19340 - 193
24X-RAY DIFFRACTION24GG217 - 266217 - 266
25X-RAY DIFFRACTION25HH1 - 201 - 20
26X-RAY DIFFRACTION26HH21 - 6621 - 66
27X-RAY DIFFRACTION27HH67 - 9467 - 94
28X-RAY DIFFRACTION28HH95 - 13595 - 135

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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