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- PDB-7coq: Hexameric Ring Complex of Engineered V1-ATPase bound to AMP-PNP: ... -

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Basic information

Entry
Database: PDB / ID: 7coq
TitleHexameric Ring Complex of Engineered V1-ATPase bound to AMP-PNP: A3(De)3_(ANP)1cat
Components
  • V-type sodium ATPase catalytic subunit A
  • V-type sodium ATPase subunit B
KeywordsMOTOR PROTEIN / Computational Design / Rotary Molecular Motor / Protein Complex
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
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 / : / 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 ...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 / : / 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. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / V-type sodium ATPase catalytic subunit A / V-type sodium ATPase subunit B
Similarity search - Component
Biological speciesEnterococcus hirae ATCC 9790 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 Å
AuthorsKosugi, T. / Tanabe, M. / Koga, N.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H05420 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101071 Japan
Japan Science and TechnologyJPMJPR13AD Japan
CitationJournal: To Be Published
Title: De Novo Design of Allosteric Control into Rotary Motor V1-ATPase by Restoring Lost Function
Authors: Kosugi, T. / Iida, T. / Tanabe, M. / Iino, R. / Koga, N.
History
DepositionAug 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)351,7618
Polymers351,2306
Non-polymers5312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, A subunit (chain ID=A, B and C) and designed B subunit (chain ID =D, E, and F) form hexameric complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22100 Å2
ΔGint-75 kcal/mol
Surface area117650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.445, 124.486, 131.339
Angle α, β, γ (deg.)90.00, 93.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 66059.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae ATCC 9790 (bacteria)
Strain: ATCC 9790 / 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: 51017.219 Da / Num. of mol.: 3
Mutation: S151G, G152P, S153P, L155A, P156G, G157K, K158S, E159A, T248E, Q339S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae ATCC 9790 (bacteria)
Strain: ATCC 9790 / Gene: ntpB, EHR_08265 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08637
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Has ligand of interestY

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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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl (pH 8.5), 22% PEG 3350 and 0.4 M Ammonium Acetate

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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 EIGER X 4M / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.44→46.34 Å / Num. obs: 53244 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.3
Reflection shellResolution: 3.44→3.55 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4602 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845)refinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7COP

7cop
PDB Unreleased entry


Resolution: 3.44→46.34 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 2379 4.47 %
Rwork0.2126 --
obs0.2142 53206 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.44→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24028 0 32 0 24060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724471
X-RAY DIFFRACTIONf_angle_d0.9933104
X-RAY DIFFRACTIONf_dihedral_angle_d18.0583360
X-RAY DIFFRACTIONf_chiral_restr0.0743726
X-RAY DIFFRACTIONf_plane_restr0.0074335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.44-3.510.35511360.31472954X-RAY DIFFRACTION100
3.51-3.590.33371240.28183005X-RAY DIFFRACTION100
3.59-3.670.33461200.27213016X-RAY DIFFRACTION100
3.67-3.760.33711110.25652996X-RAY DIFFRACTION100
3.76-3.860.28341220.2562982X-RAY DIFFRACTION100
3.86-3.980.28681340.24542932X-RAY DIFFRACTION99
3.98-4.110.28491520.24182958X-RAY DIFFRACTION100
4.11-4.250.25751700.22122944X-RAY DIFFRACTION100
4.25-4.420.24481330.19633025X-RAY DIFFRACTION100
4.42-4.620.23211160.18472998X-RAY DIFFRACTION100
4.62-4.870.21061280.1823001X-RAY DIFFRACTION100
4.87-5.170.22361330.20253020X-RAY DIFFRACTION100
5.17-5.570.23351540.21752946X-RAY DIFFRACTION100
5.57-6.130.26521570.22082980X-RAY DIFFRACTION100
6.13-7.010.28071900.22532992X-RAY DIFFRACTION100
7.01-8.830.23191610.20053004X-RAY DIFFRACTION100
8.83-46.340.19931380.17373074X-RAY DIFFRACTION100

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