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- EMDB-21229: Cryo-electron microscopy structures of a gonococcal multidrug eff... -

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Basic information

Entry
Database: EMDB / ID: EMD-21229
TitleCryo-electron microscopy structures of a gonococcal multidrug efflux pump illuminate a mechanism of erythromycin drug recognition
Map dataStructure of a gonococcal multidrug efflux pump
Sample
  • Complex: MtrD efflux pump with bound erythromycin
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: ERYTHROMYCIN A
KeywordsEfflux / pump / erythromycin / MEMBRANE PROTEIN
Function / homology
Function and homology information


efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane
Similarity search - Function
Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
: / Efflux pump membrane transporter
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsLyu M / Moseng MA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145069 United States
CitationJournal: Mbio / Year: 2020
Title: Cryo-EM Structures of a Gonococcal Multidrug Efflux Pump Illuminate a Mechanism of Drug Recognition and Resistance.
Authors: Lyu M / Moseng MA / Reimche JL / Holley CL / Dhulipala V / Su CC / Shafer WM / Yu EW
History
DepositionJan 22, 2020-
Header (metadata) releaseFeb 12, 2020-
Map releaseJul 1, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vkt
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Downloads & links

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Map

FileDownload / File: emd_21229.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of a gonococcal multidrug efflux pump
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-21.50149 - 45.424796999999998
Average (Standard dev.)0.000000000003536 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-21.50145.4250.000

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Supplemental data

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Sample components

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Entire : MtrD efflux pump with bound erythromycin

EntireName: MtrD efflux pump with bound erythromycin
Components
  • Complex: MtrD efflux pump with bound erythromycin
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: ERYTHROMYCIN A

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Supramolecule #1: MtrD efflux pump with bound erythromycin

SupramoleculeName: MtrD efflux pump with bound erythromycin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Neisseria gonorrhoeae (bacteria)

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Macromolecule #1: Efflux pump membrane transporter

MacromoleculeName: Efflux pump membrane transporter / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Neisseria gonorrhoeae (bacteria)
Molecular weightTheoretical: 111.643969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKFFIDRPI FAWVISIFII AAGIFGIKSL PVSQYPSVAA PTITLHAIYP GASAQVMEGS VLSVIERNMN GVEGLDYMST SADSSGSGS VSLTFTPDTD ENLAQVEVQN KLSEVLSTLP ATVQQYGVTV SKARSNFLMI VMLSSDVQST EEMNDYAQRN V VPELQRIE ...String:
MAKFFIDRPI FAWVISIFII AAGIFGIKSL PVSQYPSVAA PTITLHAIYP GASAQVMEGS VLSVIERNMN GVEGLDYMST SADSSGSGS VSLTFTPDTD ENLAQVEVQN KLSEVLSTLP ATVQQYGVTV SKARSNFLMI VMLSSDVQST EEMNDYAQRN V VPELQRIE GVGQVRLFGA QRAMRIWVDP KKLQNYNLSF ADVGSALSAQ NIQISAGSIG SLPAVRGQTV TATVTAQGQL GT AEEFGNV ILRANTDGSN IYLKDVAKVG LGMEDYSSST RLNGVNTTGM AVMLSNSGNA MATAKAVKER LAVLEKYFPQ GMS WKTPYD TSKFVEISIE KVIHTLIEAM VLVFVVMYLF LQNIRYTLIP TIVVPISLLG GFAFISYMGM SINVLTMFAM ILVI GIVVD DAIVVVENVE RIMAGEGLPP KEATKKAMGQ ISGAVIGITA VLISVFVPLA MFSGAAGNIY KQFALTMASS IAFSA FLAL TLTPALCATM LKTIPKGHHE EKKGFFGWFN KKFDSWTHGY EGRVAKVLRK TFRMMVVYIG LAVVGVFLFM RLPTSF LPT EDQGFVMVSV QLPAGATKER TDATLAQVTQ LAKSIPEIEN IITVSGFSFS GSGQNMAMGF AILKDWNERT ASGSDAV AV AGKLTGMMMG TLKDGFGIAV VPPPILELGN GSGLSINLQD RNNTGHTALL AKRNELIQKM RASGLFDPST VRAGGLED S PQLKIDINRA AAAAQGVSFA DIRTALASAL SSSYVSDFPN QGRLQRVMVQ ADGDARMQPA DILNLTVPNS SGIAVPLSS IATVSWQMGT EQSVRFNGYP AMELSGSPAT GVSTGQAMEA VQKMVDELGS GYSLEWGGQS REEAKGGSQT IALYALAAVA VFLVLAALY ESWSIPLAVL LVMPLGLAGA AAGVTGRNLF EGLLGSVPSF ANDIYFQVGF VTVMGLSAKN AILIIEFAKD L QAQGKSAV EAALEAARLR FRPIIMTSFA FILGVVPLYI AGGASSASQR AIGTTVFWGM LIGTLLSVFL VPLFYVVVRK FF KETAHE

UniProtKB: UNIPROTKB: A0A4T9VBR9

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Macromolecule #2: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 2 / Number of copies: 23 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #3: ERYTHROMYCIN A

MacromoleculeName: ERYTHROMYCIN A / type: ligand / ID: 3 / Number of copies: 1 / Formula: ERY
Molecular weightTheoretical: 733.927 Da
Chemical component information

ChemComp-ERY:
ERYTHROMYCIN A / antibiotic*YM

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1507208
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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