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- EMDB-71880: NorA in outward-open conformation bound to inhibitor IMP2380 -

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Basic information

Entry
Database: EMDB / ID: EMD-71880
TitleNorA in outward-open conformation bound to inhibitor IMP2380
Map data
Sample
  • Complex: NorA-BRIL in complex with IMP2380, BAG2 (Fab), and anti-kappa VHH domain
    • Protein or peptide: Quinolone resistance protein NorA, Soluble cytochrome b562 chimera
  • Ligand: (3E)-3-(1,3-benzothiazol-2-yl)-4-[3-(4-chlorophenyl)-1-methyl-1H-pyrazol-4-yl]but-3-enoic acid
Keywordsefflux pump / membrane protein / TRANSPORT PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


transmembrane transporter activity / electron transport chain / electron transfer activity / periplasmic space / iron ion binding / heme binding / plasma membrane
Similarity search - Function
: / Tetracycline resistance protein TetA/multidrug resistance protein MdtG / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Soluble cytochrome b562 / Quinolone resistance protein NorA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsSuwatthee T / Gray JL / Ledger EVK / Wang D / Edwards A / Tate EW / Traaseth NJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI165782 United States
CitationJournal: To Be Published
Title: Small molecule inhibitors of the NorA multidrug efflux pump potentiate antibiotic activity by binding the outward-open conformation
Authors: Gray JL / Ledger EVK / Suwatthee T / Lanyon-Hogg T / Burden TJ / Arvaniti K / Sefton A / Papagora LE / Clarke TB / Riley J / Pinto EG / Cunningham F / Gilbert IH / Gray D / Wang D / Read KD ...Authors: Gray JL / Ledger EVK / Suwatthee T / Lanyon-Hogg T / Burden TJ / Arvaniti K / Sefton A / Papagora LE / Clarke TB / Riley J / Pinto EG / Cunningham F / Gilbert IH / Gray D / Wang D / Read KD / Traaseth NJ / Edwards A / Tate EW
History
DepositionJul 31, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71880.png

Downloads & links

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Map

FileDownload / File: emd_71880.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.0
Minimum - Maximum-48.561905000000003 - 82.688159999999996
Average (Standard dev.)0.00052898156 (±0.89201945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71880_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71880_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NorA-BRIL in complex with IMP2380, BAG2 (Fab), and anti-kappa VHH...

EntireName: NorA-BRIL in complex with IMP2380, BAG2 (Fab), and anti-kappa VHH domain
Components
  • Complex: NorA-BRIL in complex with IMP2380, BAG2 (Fab), and anti-kappa VHH domain
    • Protein or peptide: Quinolone resistance protein NorA, Soluble cytochrome b562 chimera
  • Ligand: (3E)-3-(1,3-benzothiazol-2-yl)-4-[3-(4-chlorophenyl)-1-methyl-1H-pyrazol-4-yl]but-3-enoic acid

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Supramolecule #1: NorA-BRIL in complex with IMP2380, BAG2 (Fab), and anti-kappa VHH...

SupramoleculeName: NorA-BRIL in complex with IMP2380, BAG2 (Fab), and anti-kappa VHH domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Staphylococcus aureus (bacteria) / Location in cell: membrane
Molecular weightTheoretical: 122.72 KDa

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Macromolecule #1: Quinolone resistance protein NorA, Soluble cytochrome b562 chimera

MacromoleculeName: Quinolone resistance protein NorA, Soluble cytochrome b562 chimera
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 54.183363 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNKQIFVLYF NIFLIFLGIG LVIPVLPVYL KDLGLTGSDL GLLVAAFALS QMIISPFGGT LADKLGKKLI ICIGLILFSV SEFMFAVGH NFSVLMLSRV IGGMSAGMVM PGVTGLIADI SPSHQKAKNF GYMSAIINSG FILGPGIGGF MAEVSHRMPF Y FAGALGIL ...String:
MNKQIFVLYF NIFLIFLGIG LVIPVLPVYL KDLGLTGSDL GLLVAAFALS QMIISPFGGT LADKLGKKLI ICIGLILFSV SEFMFAVGH NFSVLMLSRV IGGMSAGMVM PGVTGLIADI SPSHQKAKNF GYMSAIINSG FILGPGIGGF MAEVSHRMPF Y FAGALGIL AFIMSIVLIH DPKKSTTSGF QKLEPQLLTK INWKVFITPV ILTLVLSFGL SAFETLYSLY TADKVNYSPK DI SIAITGG GIFGALFQIY FFDKFMKYFS ELTFIAWSLL YSVVVLILLV FANDYWSIML ISFVVFIGFD MIRPAITNYF SNI AGERQG FAGGLNSTFT SMGNFIGPLI AGALFDVHIE APIYMAIGVS LAGVVIVLIE KQHRAAAADL EDNWETLNDN LKVI EKADN AAQVKDALTK MRAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQI DDALKLANEG KVKEAQAAAE QLKTT RNAY IQKYLENLYF Q

UniProtKB: Quinolone resistance protein NorA, Soluble cytochrome b562

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Macromolecule #2: (3E)-3-(1,3-benzothiazol-2-yl)-4-[3-(4-chlorophenyl)-1-methyl-1H-...

MacromoleculeName: (3E)-3-(1,3-benzothiazol-2-yl)-4-[3-(4-chlorophenyl)-1-methyl-1H-pyrazol-4-yl]but-3-enoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1CLB
Molecular weightTheoretical: 409.889 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5.24 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMNa2HPO4sodium phosphate
100.0 mMNaClsodium chloride

Details: NorA-BRIL reconstituted in PMAL-C8 amphipol
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 13288 / Average exposure time: 1.8 sec. / Average electron dose: 47.12 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.4 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8279459
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 634207
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 1
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL / Overall B value: 112.1
Output model

PDB-9pv0:
NorA in outward-open conformation bound to inhibitor IMP2380

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