[English] 日本語
Yorodumi
- PDB-9lrr: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreduc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lrr
TitleCryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-G141A mutant from Vibrio cholerae with bound korormicin A
Components(Na(+)-translocating NADH-quinone reductase subunit ...) x 6
KeywordsMEMBRANE PROTEIN / Na+-NQR / Na+ transporter / inhibitor / oxidoreductase / drug resistant
Function / homology
Function and homology information


riboflavin binding / NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / FAD binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / transmembrane transport / FMN binding ...riboflavin binding / NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / FAD binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / transmembrane transport / FMN binding / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / : / : / NqrA N-terminal barrel-sandwich hybrid domain / NQRA C-terminal domain / NqrA second alpha/beta domain ...Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / : / : / NqrA N-terminal barrel-sandwich hybrid domain / NQRA C-terminal domain / NqrA second alpha/beta domain / Na(+)-translocating NADH-quinone reductase subunit C / Na(+)-translocating NADH-quinone reductase subunit F / NqrDE/RnfAE / Ion-translocating oxidoreductase NqrB/RnfD / : / Rnf-Nqr subunit, membrane protein / NQR2, RnfD, RnfE family / FMN-binding / FMN-binding domain / FMN_bind / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Korormicin / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / RIBOFLAVIN / Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit F / Na(+)-translocating NADH-quinone reductase subunit E ...FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Korormicin / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / RIBOFLAVIN / Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit F / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-translocating NADH-quinone reductase subunit C
Similarity search - Component
Biological speciesVibrio cholerae O395 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsIshikawa-Fukuda, M. / Kishikawa, J. / Kato, T. / Murai, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K08729 Japan
Japan Society for the Promotion of Science (JSPS)22H02273 Japan
Japan Society for the Promotion of Science (JSPS)22KJ1795 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121001 Japan
CitationJournal: Biochemistry / Year: 2025
Title: Structural Elucidation of the Mechanism for Inhibitor Resistance in the Na-Translocating NADH-Ubiquinone Oxidoreductase from .
Authors: Moe Ishikawa-Fukuda / Jun-Ichi Kishikawa / Takahiro Masuya / Takeshi Ito / Nicole L Butler / Danielle McFee / Takayuki Kato / Blanca Barquera / Hideto Miyoshi / Masatoshi Murai /
Abstract: Na-translocating NADH-ubiquinone oxidoreductase (Na-NQR) is a unique redox-driven Na-pump. Since this enzyme is exclusively found in prokaryotes, including the human pathogens and , it is a ...Na-translocating NADH-ubiquinone oxidoreductase (Na-NQR) is a unique redox-driven Na-pump. Since this enzyme is exclusively found in prokaryotes, including the human pathogens and , it is a promising target for highly selective antibiotics. Korormicin A, a natural product, and a specific and potent inhibitor of Na-NQR, may become a lead compound for the relevant drug design. We previously showed that the G141A mutation in the NqrB subunit (NqrB-G141A) confers moderate resistance to korormicin A (about 100-fold). However, the efficiency of photoaffinity labeling of the mutant enzyme by a photoreactive korormicin derivative was the same as in the wild-type enzyme. Because of these apparently conflicting results, the molecular mechanism underlying the korormicin A-resistance remains elusive. In the present study, we determined the cryo-EM structure of the NqrB-G141A mutant in the presence of bound korormicin A, and compared it to the corresponding structure from the wild-type enzyme. The toxophoric moiety of korormicin A binds to the mutant enzyme similarly to how it binds to the wild type. However, the added bulk of the alanine-141 excludes the alkyl side chain from the binding cavity, resulting in a decrease in the binding affinity. In fact, isothermal titration calorimetry revealed that the binding affinity of korormicin to the NqrB-G141A mutant is significantly weaker compared to the wild-type. Altogether, we conclude that the inhibitory potency of korormicin A is weaker in the NqrB-G141A mutant due to the decrease in its binding affinity to the altered binding cavity.
History
DepositionFeb 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 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_ASTM / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Na(+)-translocating NADH-quinone reductase subunit A
B: Na(+)-translocating NADH-quinone reductase subunit B
C: Na(+)-translocating NADH-quinone reductase subunit C
D: Na(+)-translocating NADH-quinone reductase subunit D
E: Na(+)-translocating NADH-quinone reductase subunit E
F: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,42418
Polymers212,0156
Non-polymers5,40912
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Na(+)-translocating NADH-quinone reductase subunit ... , 6 types, 6 molecules ABCDEF

#1: Protein Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-NQR subunit A / Na(+)-translocating NQR subunit A / NQR complex subunit A / NQR-1 subunit A


Mass: 48680.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: nqrA, VC0395_A1884, VC395_2411 / Production host: Vibrio cholerae O395 (bacteria)
References: UniProt: A5F5X1, NADH:ubiquinone reductase (Na+-transporting)
#2: Protein Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-NQR subunit B / Na(+)-translocating NQR subunit B / NQR complex subunit B / NQR-1 subunit B


Mass: 45404.906 Da / Num. of mol.: 1 / Mutation: G141A
Source method: isolated from a genetically manipulated source
Details: NqrB-G141A / Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: nqrB, VC0395_A1883, VC395_2410 / Production host: Vibrio cholerae O395 (bacteria)
References: UniProt: A5F5X0, NADH:ubiquinone reductase (Na+-transporting)
#3: Protein Na(+)-translocating NADH-quinone reductase subunit C / Na(+)-NQR subunit C / Na(+)-translocating NQR subunit C / NQR complex subunit C / NQR-1 subunit C


Mass: 27652.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: nqrC, VC0395_A1882, VC395_2409 / Production host: Vibrio cholerae O395 (bacteria)
References: UniProt: A5F5Y7, NADH:ubiquinone reductase (Na+-transporting)
#4: Protein Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-NQR subunit D / Na(+)-translocating NQR subunit D / NQR complex subunit D / NQR-1 subunit D


Mass: 22853.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: nqrD, VC0395_A1881, VC395_2408 / Production host: Vibrio cholerae O395 (bacteria)
References: UniProt: A5F5Y6, NADH:ubiquinone reductase (Na+-transporting)
#5: Protein Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-NQR subunit E / Na(+)-translocating NQR subunit E / NQR complex subunit E / NQR-1 subunit E


Mass: 21481.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: nqrE, VC0395_A1880, VC395_2407 / Production host: Vibrio cholerae O395 (bacteria)
References: UniProt: A5F5Y5, NADH:ubiquinone reductase (Na+-transporting)
#6: Protein Na(+)-translocating NADH-quinone reductase subunit F / Na(+)-NQR subunit F / Na(+)-translocating NQR subunit F / NQR complex subunit F / NQR-1 subunit F


Mass: 45942.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: nqrF, VC0395_A1879, VC395_2406 / Production host: Vibrio cholerae O395 (bacteria)
References: UniProt: A5F5Y4, NADH:ubiquinone reductase (Na+-transporting)

-
Sugars , 1 types, 2 molecules

#9: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 8 types, 46 molecules

#7: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#8: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6
#10: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#11: Chemical ChemComp-IQT / Korormicin


Mass: 433.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H39NO5 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#13: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#14: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Na(+)-translocating NADH-quinone reductase / Type: COMPLEX / Details: NqrB-G141A mutant / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightValue: 0.214 MDa / Experimental value: NO
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Source (recombinant)Organism: Vibrio cholerae O395 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMtris-hcl hydrochlorideC4H13Cl2NO31
30.05 %n-DODECYL-beta-D-MALTOSIDEC24H46O111
41 mMEthylenediaminetetraacetic acidC10H16N2O81
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 magnification: 81000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 0.131 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Spherical aberration corrector: Image corrector

-
Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCv3.3.1particle selectionTopaz Extract
2SerialEM4image acquisition
4cryoSPARCv3.3.1CTF correction
7Coot0.9model fitting
9cryoSPARC3.3.1initial Euler assignment
10cryoSPARC3.3.1final Euler assignment
11cryoSPARCv3.3.1classification
12cryoSPARCv3.3.13D reconstructionNon-uniform refinement
13PHENIX1.21_5207model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1961776
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1035957 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7XK7

7xk7


Accession code: 7XK7 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.68 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215414
ELECTRON MICROSCOPYf_angle_d0.48920892
ELECTRON MICROSCOPYf_dihedral_angle_d7.9392542
ELECTRON MICROSCOPYf_chiral_restr0.0412353
ELECTRON MICROSCOPYf_plane_restr0.0042612

+
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