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- PDB-8wci: Cryo-EM structure of the inhibitor-bound Vo complex from Enteroco... -

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Basic information

Entry
Database: PDB / ID: 8wci
TitleCryo-EM structure of the inhibitor-bound Vo complex from Enterococcus hirae
Components(V-type sodium ATPase subunit ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / V-ATPase / Na+-transporting / membrane protein / ATP hydrolyses / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / sodium ion transport / proton-transporting ATPase activity, rotational mechanism / ATPase binding / identical protein binding / plasma membrane
Similarity search - Function
V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
CARDIOLIPIN / : / V-type sodium ATPase subunit I / V-type sodium ATPase subunit K
Similarity search - Component
Biological speciesEnterococcus hirae ATCC 9790 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsSuzuki, K. / Mikuriya, S. / Adachi, N. / Kawasaki, M. / Senda, T. / Moriya, T. / Murata, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Na-V-ATPase inhibitor curbs VRE growth and unveils Na pathway structure.
Authors: Kano Suzuki / Yoshiyuki Goto / Akihiro Otomo / Kouki Shimizu / Shohei Abe / Katsuhiko Moriyama / Satoshi Yasuda / Yusuke Hashimoto / Jun Kurushima / Sho Mikuriya / Fabiana L Imai / Naruhiko ...Authors: Kano Suzuki / Yoshiyuki Goto / Akihiro Otomo / Kouki Shimizu / Shohei Abe / Katsuhiko Moriyama / Satoshi Yasuda / Yusuke Hashimoto / Jun Kurushima / Sho Mikuriya / Fabiana L Imai / Naruhiko Adachi / Masato Kawasaki / Yumi Sato / Satoshi Ogasawara / So Iwata / Toshiya Senda / Mitsunori Ikeguchi / Haruyoshi Tomita / Ryota Iino / Toshio Moriya / Takeshi Murata /
Abstract: Vancomycin-resistant Enterococcus faecium (VRE) is a major cause of nosocomial infections, particularly endocarditis and sepsis. With the diminishing effectiveness of antibiotics against VRE, new ...Vancomycin-resistant Enterococcus faecium (VRE) is a major cause of nosocomial infections, particularly endocarditis and sepsis. With the diminishing effectiveness of antibiotics against VRE, new antimicrobial agents are urgently needed. Our previous research demonstrated the crucial role of Na-transporting V-ATPase in Enterococcus hirae for growth under alkaline conditions. In this study, we identified a compound, V-161, from 70,600 compounds, which markedly inhibits E. hirae V-ATPase activity. V-161 not only inhibits VRE growth in alkaline conditions but also significantly suppresses VRE colonization in the mouse small intestine. Furthermore, we unveiled the high-resolution structure of the membrane V part due to V-161 binding. V-161 binds to the interface of the c-ring and a-subunit, constituting the Na transport pathway in the membrane, thereby halting its rotation. This structural insight presents potential avenues for developing therapeutic agents for VRE treatment and elucidates the Na transport pathway and mechanism.
History
DepositionSep 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-type sodium ATPase subunit K
B: V-type sodium ATPase subunit K
C: V-type sodium ATPase subunit K
D: V-type sodium ATPase subunit K
E: V-type sodium ATPase subunit K
F: V-type sodium ATPase subunit K
G: V-type sodium ATPase subunit K
H: V-type sodium ATPase subunit K
I: V-type sodium ATPase subunit K
J: V-type sodium ATPase subunit K
P: V-type sodium ATPase subunit I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,73326
Polymers236,95511
Non-polymers7,77815
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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V-type sodium ATPase subunit ... , 2 types, 11 molecules ABCDEFGHIJP

#1: Protein
V-type sodium ATPase subunit K / Na(+)-translocating ATPase subunit K / Sodium ATPase proteolipid component


Mass: 16043.918 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae ATCC 9790 (bacteria)
Gene: ntpK, ntpN, EHR_08240 / Production host: Escherichia coli (E. coli) / References: UniProt: P43457
#2: Protein V-type sodium ATPase subunit I


Mass: 76515.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae ATCC 9790 (bacteria)
Gene: ntpI / Production host: Escherichia coli (E. coli) / References: UniProt: P43439

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Non-polymers , 4 types, 239 molecules

#3: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-W3K / N,N-dimethyl-4-(5-methyl-1H-benzimidazol-2-yl)aniline


Mass: 251.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: V-ATPase / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.735 MDa / Experimental value: NO
Source (natural)Organism: Enterococcus hirae ATCC 9790 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
250 mMTris hydrochloride acidTris-HCl1
35 mMmagnesium sulfateMgSO41
40.005 %lauryl maltose neopentyl glycolLMNG1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV

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Processing

EM software
IDNameVersionCategory
1RELION3.1.3particle selection
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
9RELION3.1.3initial Euler assignment
10RELION3.1.3final Euler assignment
12RELION3.1.33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1008654
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225359 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeInitial refinement model-IDSource nameTypeDetails
12BL2

2bl2

2BL21PDBexperimental model
2SwissModel6LY9
3SwissModel6M0S
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 32.58 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007214934
ELECTRON MICROSCOPYf_angle_d0.825720230
ELECTRON MICROSCOPYf_chiral_restr0.05462440
ELECTRON MICROSCOPYf_plane_restr0.00512493
ELECTRON MICROSCOPYf_dihedral_angle_d11.7982385

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