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- PDB-8igw: Hexameric Ring Complex of Engineered V1-ATPase bound to 4 ADPs: A... -

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Basic information

Entry
Database: PDB / ID: 8igw
TitleHexameric Ring Complex of Engineered V1-ATPase bound to 4 ADPs: A3(De)3_(ADP)3cat,1non-cat, Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP)3cat,2non-cat
Components
  • V-type sodium ATPase catalytic subunit A
  • V-type sodium ATPase subunit B
KeywordsMOTOR PROTEIN / Computational Design / Rotary Molecular Motor / 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
ADENOSINE-5'-DIPHOSPHATE / 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: 4.2 Å
AuthorsKosugi, T. / Tanabe, M. / Koga, N.
Funding support Japan, 4items
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
Japan Science and TechnologyJPMJPR20E6 Japan
CitationJournal: Nat.Chem. / Year: 2023
Title: Design of allosteric sites into rotary motor V 1 -ATPase by restoring lost function of pseudo-active sites.
Authors: Kosugi, T. / Iida, T. / Tanabe, M. / Iino, R. / Koga, N.
History
DepositionFeb 21, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionJul 12, 2023ID: 7COS
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 12, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details
Item: _pdbx_database_related.content_type / _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
G: V-type sodium ATPase catalytic subunit A
H: V-type sodium ATPase catalytic subunit A
I: V-type sodium ATPase catalytic subunit A
J: V-type sodium ATPase subunit B
K: V-type sodium ATPase subunit B
L: V-type sodium ATPase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)706,52430
Polymers702,46112
Non-polymers4,06418
Water00
1
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)353,03614
Polymers351,2306
Non-polymers1,8068
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24840 Å2
ΔGint-144 kcal/mol
Surface area119170 Å2
MethodPISA
2
G: V-type sodium ATPase catalytic subunit A
H: V-type sodium ATPase catalytic subunit A
I: V-type sodium ATPase catalytic subunit A
J: V-type sodium ATPase subunit B
K: V-type sodium ATPase subunit B
L: V-type sodium ATPase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,48816
Polymers351,2306
Non-polymers2,25810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25590 Å2
ΔGint-159 kcal/mol
Surface area121030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.407, 125.077, 180.914
Angle α, β, γ (deg.)90.000, 93.826, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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.: 6
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.: 6
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl (pH 8.5), 20% PEG 3350, 0.2M 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: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 4.2→48.92 Å / Num. obs: 58670 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 116.21 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.095 / Net I/σ(I): 7.2
Reflection shellResolution: 4.2→4.32 Å / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4576 / CC1/2: 0.764 / Rpim(I) all: 0.423

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→48.92 Å / SU ML: 0.5669 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1885
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2811 2921 4.98 %
Rwork0.242 55694 -
obs0.2439 58615 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 153.47 Å2
Refinement stepCycle: LAST / Resolution: 4.2→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47540 0 252 0 47792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002848610
X-RAY DIFFRACTIONf_angle_d0.651365796
X-RAY DIFFRACTIONf_chiral_restr0.04647385
X-RAY DIFFRACTIONf_plane_restr0.00428597
X-RAY DIFFRACTIONf_dihedral_angle_d18.233618356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.270.30751830.27562595X-RAY DIFFRACTION99.96
4.27-4.340.30271590.27272592X-RAY DIFFRACTION99.96
4.34-4.420.31591410.26582658X-RAY DIFFRACTION100
4.42-4.510.27971050.25262647X-RAY DIFFRACTION99.96
4.51-4.60.27841070.2442692X-RAY DIFFRACTION99.96
4.6-4.70.24351590.24052588X-RAY DIFFRACTION99.93
4.7-4.810.30691450.24282623X-RAY DIFFRACTION100
4.81-4.930.31981360.23782655X-RAY DIFFRACTION99.96
4.93-5.060.27131420.25612635X-RAY DIFFRACTION100
5.06-5.210.34441580.2642669X-RAY DIFFRACTION100
5.21-5.380.29531670.26352572X-RAY DIFFRACTION99.93
5.38-5.570.34431330.27392626X-RAY DIFFRACTION100
5.57-5.790.34811230.28022684X-RAY DIFFRACTION100
5.79-6.050.3311270.27512676X-RAY DIFFRACTION100
6.06-6.370.34571260.2632643X-RAY DIFFRACTION100
6.37-6.770.25971690.24112630X-RAY DIFFRACTION100
6.77-7.290.29431510.25292685X-RAY DIFFRACTION100
7.29-8.020.27771360.23762633X-RAY DIFFRACTION100
8.02-9.180.20951280.20172709X-RAY DIFFRACTION100
9.18-11.540.2161130.18942721X-RAY DIFFRACTION99.72
11.54-48.920.27161130.24032761X-RAY DIFFRACTION99.24

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