[English] 日本語
Yorodumi
- PDB-8igv: Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8igv
TitleHexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP-Pi)1cat(ADP)2cat,2non-cat
Components(V-type sodium ATPase ...) x 2
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 / PHOSPHATE ION / 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: 3.15 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: 7COR
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)353,58317
Polymers351,2306
Non-polymers2,35311
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25630 Å2
ΔGint-156 kcal/mol
Surface area113610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.667, 126.736, 123.649
Angle α, β, γ (deg.)90.000, 93.934, 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

-
Components

-
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: 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

-
Non-polymers , 4 types, 128 molecules

#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / 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.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl (pH 8.5), 24% PEG 3350, 0.2 M Ammonium Acetate

-
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: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.15→48.38 Å / Num. obs: 63835 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 55.73 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.087 / Net I/σ(I): 7.7
Reflection shellResolution: 3.15→3.23 Å / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2 / Num. unique obs: 4482 / CC1/2: 0.569 / Rpim(I) all: 0.49

-
Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→48.38 Å / SU ML: 0.3815 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0638
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2681 3152 4.94 %
Rwork0.2113 60647 -
obs0.214 63799 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.31 Å2
Refinement stepCycle: LAST / Resolution: 3.15→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23997 0 145 117 24259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004924562
X-RAY DIFFRACTIONf_angle_d0.939233238
X-RAY DIFFRACTIONf_chiral_restr0.0563727
X-RAY DIFFRACTIONf_plane_restr0.00574334
X-RAY DIFFRACTIONf_dihedral_angle_d23.20469322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.20.3151540.27772586X-RAY DIFFRACTION100
3.2-3.250.34191590.28012597X-RAY DIFFRACTION99.96
3.25-3.30.32981260.27582642X-RAY DIFFRACTION99.96
3.3-3.360.34031680.26262610X-RAY DIFFRACTION99.96
3.36-3.420.3351510.25692609X-RAY DIFFRACTION99.93
3.42-3.480.31021480.24832603X-RAY DIFFRACTION99.96
3.48-3.550.30121560.23972589X-RAY DIFFRACTION99.96
3.55-3.630.28521270.23232674X-RAY DIFFRACTION99.96
3.63-3.720.26151400.22362607X-RAY DIFFRACTION99.93
3.72-3.810.24861150.21562635X-RAY DIFFRACTION100
3.81-3.910.27721060.21182653X-RAY DIFFRACTION100
3.91-4.030.30631450.22122626X-RAY DIFFRACTION100
4.03-4.160.31311440.22772623X-RAY DIFFRACTION100
4.16-4.310.23831570.19362606X-RAY DIFFRACTION100
4.31-4.480.21591340.17822650X-RAY DIFFRACTION100
4.48-4.680.21121270.17122654X-RAY DIFFRACTION100
4.68-4.930.26421260.17312643X-RAY DIFFRACTION100
4.93-5.240.23391470.19632647X-RAY DIFFRACTION100
5.24-5.640.25231380.20682634X-RAY DIFFRACTION100
5.64-6.210.23881490.2182629X-RAY DIFFRACTION100
6.21-7.10.30091050.20782697X-RAY DIFFRACTION100
7.1-8.940.24121150.18222693X-RAY DIFFRACTION100
8.94-48.380.21241150.18922740X-RAY DIFFRACTION99.69

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • 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

-
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

Read more