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- PDB-7dqe: Crystal structure of the ADP-bound mutant A(S23C)3B(N64C)3 comple... -

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Basic information

Entry
Database: PDB / ID: 7dqe
TitleCrystal structure of the ADP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase
Components(V-type sodium ATPase ...) x 2
KeywordsHYDROLASE / V-ATPase / A3B3 / asymmetric structure
Function / homology
Function and homology information


Na+-transporting two-sector ATPase / sodium-transporting ATPase activity, rotational mechanism / proton motive force-driven plasma membrane ATP synthesis / sodium ion transport / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
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 / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal ...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 / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / V-type sodium ATPase catalytic subunit A / V-type sodium ATPase subunit B
Similarity search - Component
Biological speciesEnterococcus hirae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.694 Å
AuthorsMaruyama, S. / Nakamoto, K. / Suzuki, K. / Mizutani, K. / Imai, F.L. / Ishizuka-Katsura, Y. / Shirouzu, M. / Murata, T.
CitationJournal: To Be Published
Title: The Combination of High-Speed AFM and X-ray Crystallography Reveals Rotary Catalytic Mechanism of Shaftless V1-ATPase
Authors: Imamura, M. / Maruyama, S. / Nakamoto, K. / Kawai, F. / Akiyama, T. / Mizutani, K. / Suzuki, K. / Shirouzu, M. / Iino, R. / Uchihashi, T. / Ando, T. / Murata, T.
History
DepositionDec 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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: V-type sodium ATPase catalytic subunit A
B: V-type sodium ATPase catalytic subunit A
C: V-type sodium ATPase catalytic subunit A
D: V-type sodium ATPase subunit B
E: V-type sodium ATPase subunit B
F: V-type sodium ATPase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,67213
Polymers354,2216
Non-polymers1,4517
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29400 Å2
ΔGint-157 kcal/mol
Surface area109150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.030, 121.090, 231.470
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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V-type sodium ATPase ... , 2 types, 6 molecules ABCDEF

#1: Protein V-type sodium ATPase catalytic subunit A / Na(+)-translocating ATPase subunit A / V-type sodium pump catalytic subunit A


Mass: 66363.867 Da / Num. of mol.: 3 / Mutation: S23C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258) (bacteria)
Gene: ntpA, EHR_08260 / Production host: Escherichia coli (E. coli)
References: UniProt: Q08636, Na+-transporting two-sector ATPase
#2: Protein V-type sodium ATPase subunit B / Na(+)-translocating ATPase subunit B / V-type sodium pump subunit B


Mass: 51709.938 Da / Num. of mol.: 3 / Mutation: N64C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258) (bacteria)
Gene: ntpB, EHR_08265 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08637

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Non-polymers , 4 types, 198 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 7.5 / Details: 23% PEG 3350, 100mM Tris pH 7.5, 100mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.69→47.631 Å / Num. obs: 92593 / % possible obs: 98.7 % / Redundancy: 3.371 % / Biso Wilson estimate: 36.77 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.183 / Χ2: 1.065 / Net I/σ(I): 8.71 / Num. measured all: 312121
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.69-2.863.4060.642.094987114931146440.670.75598.1
2.86-3.053.3060.4672.854633414096140140.7940.55399.4
3.05-3.33.3480.3284.094382413135130890.8840.38999.6
3.3-3.613.5190.2036.834237912105120430.960.23799.5
3.61-4.033.4060.1310.253726611050109420.9810.15399
4.03-4.653.2550.0815.1731379976296400.9910.09598.8
4.65-5.693.3920.07416.3227691831581640.9930.08898.2
5.69-7.993.3330.07216.4321297655263900.9940.08597.5
7.99-47.6313.2940.03828.2312080386936670.9980.04594.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KNC

5knc


Resolution: 2.694→47.631 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 4793 5.18 %
Rwork0.2255 87789 -
obs0.2269 92582 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.16 Å2 / Biso mean: 38.8365 Å2 / Biso min: 8.06 Å2
Refinement stepCycle: final / Resolution: 2.694→47.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23813 0 89 191 24093
Biso mean--32.26 25.05 -
Num. residues----3106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224312
X-RAY DIFFRACTIONf_angle_d0.60132947
X-RAY DIFFRACTIONf_chiral_restr0.0233743
X-RAY DIFFRACTIONf_plane_restr0.0034307
X-RAY DIFFRACTIONf_dihedral_angle_d12.899058
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6942-2.72480.32391590.3067271694
2.7248-2.75690.32611770.3052290199
2.7569-2.79050.27661640.2975290299
2.7905-2.82580.33351510.3012288299
2.8258-2.8630.33731670.2962291899
2.863-2.90220.35431770.2962891100
2.9022-2.94370.33721660.2788292599
2.9437-2.98760.31061510.2908292699
2.9876-3.03430.31991750.2914289299
3.0343-3.0840.30461680.28192913100
3.084-3.13720.33881720.2742893100
3.1372-3.19420.31011690.26952945100
3.1942-3.25560.29441580.26542929100
3.2556-3.32210.28861650.25812938100
3.3221-3.39430.2761580.25662930100
3.3943-3.47320.23381580.2377294199
3.4732-3.560.28691650.2279292799
3.56-3.65630.26161430.22972943100
3.6563-3.76380.24091700.2202292799
3.7638-3.88520.25231480.2116295899
3.8852-4.0240.21771590.205290598
4.024-4.18510.23521460.2017294699
4.1851-4.37540.20731700.1814291099
4.3754-4.60590.17491550.1701296699
4.6059-4.89420.18051690.1704291698
4.8942-5.27170.22161420.1958296698
5.2717-5.80130.26131320.2066298298
5.8013-6.63890.24011400.2138296998
6.6389-8.35690.20711530.1869299297
8.3569-47.6310.19081660.1697304095
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)
12.55971.23791.34761.33181.5741.844-0.190.39750.0692-0.35260.17730.0456-0.01230.28810.02480.2667-0.0293-0.03340.25860.05390.198656.9425-4.5881-60.6081
23.0349-0.77660.7740.9061-0.55122.43190.10590.3143-0.0579-0.0721-0.1472-0.26230.080.41510.04440.2118-0.04820.0510.3033-0.0240.374579.62466.0068-56.7387
31.607-0.46150.03551.10410.64021.6503-0.0278-0.03570.15-0.00650.0062-0.1854-0.14540.18480.01770.2482-0.0264-0.02990.26380.08270.304164.024116.0736-41.4977
40.68390.12550.24782.14920.89631.35010.0472-0.23780.16010.2925-0.1012-0.0866-0.1564-0.01210.05980.3263-0.0565-0.04030.31720.03150.242658.775924.683-24.091
51.7556-0.0027-0.58630.5908-1.13194.2357-0.2519-0.0027-0.4435-0.0323-0.0013-0.06530.49780.12730.27340.25470.02890.06910.16460.0240.312343.1172-40.7217-29.679
64.78722.635-0.71162.5754-1.01311.6114-0.1908-0.1736-1.038-0.1089-0.0299-0.47530.53860.02380.2220.48690.04860.05530.32110.03650.477535.3935-54.463-8.9479
72.21310.7913-0.01181.53240.17780.66560.0922-0.3375-0.18860.1918-0.0953-0.04380.2629-0.04720.00050.2591-0.01370.0230.21290.0390.170832.2125-30.2979-3.8846
81.0689-0.2638-0.44671.52381.0912.17310.0355-0.11430.1090.0945-0.02570.0357-0.2003-0.0294-0.02350.177-0.0111-0.01150.22790.03090.190426.2881-17.2532-0.1938
92.9817-1.70090.043.30220.08390.01250.070.1726-0.0689-0.4158-0.0533-0.0821-0.0716-0.0086-0.02060.2547-0.0264-0.00050.2707-0.00190.197110.6676-20.1079-62.1828
101.52610.75190.25853.3158-1.58123.3869-0.23610.31860.0349-0.7860.35350.4290.2659-0.2217-0.11990.2945-0.0611-0.08280.2989-0.01150.3522-8.6041-4.8904-70.8145
110.9883-0.18660.22251.7683-0.3281.6152-0.0038-0.0520.13650.1598-0.01550.0772-0.2324-0.03280.00970.2117-0.03770.00910.21670.02370.1946.12854.6058-48.9805
122.35330.205-0.39443.34471.09931.03970.0212-0.46760.27511.03240.1639-0.2816-0.9338-0.1657-0.15221.08380.1042-0.0220.38710.02450.43415.462624.4515-28.7909
132.04660.44120.33982.42081.24391.8912-0.1762-0.41290.44420.98510.1140.5661-0.9859-0.26070.06951.55540.35690.24740.63210.11620.6744-5.444829.8444-23.8829
141.29780.7038-1.07814.8881-0.91170.91240.0476-0.0277-0.0850.3125-0.23960.1828-0.00870.04760.18030.3162-0.035100.3275-0.01730.225331.0794-5.6081-72.9864
151.7452-0.3755-1.12181.74650.42813.16490.08630.30750.2818-0.1202-0.0532-0.0605-0.277-0.1462-0.02870.18410.0042-0.03710.19690.07050.252734.134123.3314-60.4969
161.38090.0184-0.59971.9693-0.46611.05210.00720.08340.0377-0.0428-0.01780.12980.014-0.11170.00180.1913-0.0336-0.06460.2497-0.00180.179533.277614.1147-59.8861
172.1147-0.30880.23753.80580.85521.6788-0.032-0.48690.59070.4906-0.05730.0349-0.2572-0.12270.06880.3155-0.0094-0.02920.3319-0.07960.350132.246933.0612-38.321
182.0123-0.74580.84732.532-0.52533.2097-0.01340.3119-0.0731-0.25120.0663-0.1436-0.09220.4236-0.05930.1843-0.02090.05050.2505-0.01760.233962.4013-23.7619-42.2796
192.9197-1.04580.82142.0142-0.66912.2439-0.1222-0.28570.27620.29670.0088-0.3541-0.21320.17830.0930.2282-0.0228-0.03830.21810.00810.228559.2183-11.6475-15.2761
202.0315-0.12250.14982.0052-1.01922.7453-0.6824-1.2360.33731.26680.7598-0.0648-0.7805-0.2186-0.1021.11320.3477-0.03520.9773-0.09760.605648.33720.59959.9544
210.8944-0.6658-0.89830.95920.35361.1096-0.14510.0273-0.21410.08290.09850.13780.1985-0.08880.03190.2517-0.07080.03050.2843-0.01190.333415.6783-39.6591-40.1618
220.4084-0.45580.59111.34760.44712.1155-0.1418-0.1562-0.02750.19840.12180.2178-0.0188-0.44560.05560.1737-0.00280.06140.23690.04030.2155-2.3518-17.4185-25.9957
230.744-0.27780.09691.82010.21141.5766-0.0184-0.16210.0540.20670.01620.0918-0.1698-0.1065-0.00260.1980.00160.02840.25750.04030.17723.6117-10.0732-22.1338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 90 )A1 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 192 )A91 - 192
3X-RAY DIFFRACTION3chain 'A' and (resid 193 through 330 )A193 - 330
4X-RAY DIFFRACTION4chain 'A' and (resid 331 through 584 )A331 - 584
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 90 )B1 - 90
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 185 )B91 - 185
7X-RAY DIFFRACTION7chain 'B' and (resid 186 through 284 )B186 - 284
8X-RAY DIFFRACTION8chain 'B' and (resid 285 through 584 )B285 - 584
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 90 )C1 - 90
10X-RAY DIFFRACTION10chain 'C' and (resid 91 through 192 )C91 - 192
11X-RAY DIFFRACTION11chain 'C' and (resid 193 through 452 )C193 - 452
12X-RAY DIFFRACTION12chain 'C' and (resid 453 through 538 )C453 - 538
13X-RAY DIFFRACTION13chain 'C' and (resid 539 through 584 )C539 - 584
14X-RAY DIFFRACTION14chain 'D' and (resid 7 through 85 )D7 - 85
15X-RAY DIFFRACTION15chain 'D' and (resid 86 through 187 )D86 - 187
16X-RAY DIFFRACTION16chain 'D' and (resid 188 through 305 )D188 - 305
17X-RAY DIFFRACTION17chain 'D' and (resid 306 through 452 )D306 - 452
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 85 )E1 - 85
19X-RAY DIFFRACTION19chain 'E' and (resid 86 through 351 )E86 - 351
20X-RAY DIFFRACTION20chain 'E' and (resid 352 through 454 )E352 - 454
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 106 )F1 - 106
22X-RAY DIFFRACTION22chain 'F' and (resid 107 through 187 )F107 - 187
23X-RAY DIFFRACTION23chain 'F' and (resid 188 through 454 )F188 - 454

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