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- EMDB-39532: Cryo-EM Structure of AdeG from Acinetobacter baumannii -

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Basic information

Entry
Database: EMDB / ID: EMD-39532
TitleCryo-EM Structure of AdeG from Acinetobacter baumannii
Map data
Sample
  • Complex: Multidrug efflux RND transporter permease subunit AdeG
    • Protein or peptide: Cation/multidrug efflux pump
  • Ligand: DODECYL-BETA-D-MALTOSIDE
KeywordsEfflux Pump / Acinetobacter baumannii / Multidrug Resistance / AdeG / MEMBRANE PROTEIN
Function / homology:
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsOuyang Z / Wen Y / Zhu L
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82102402 China
National Natural Science Foundation of China (NSFC)82072237 China
National Natural Science Foundation of China (NSFC)32170187 China
National Natural Science Foundation of China (NSFC)31600593 China
CitationJournal: Structure / Year: 2025
Title: Cryo-EM structure and complementary drug efflux activity of the Acinetobacter baumannii multidrug efflux pump AdeG.
Authors: Zhenlin Ouyang / Wenbo He / Di Wu / Hao An / Lei Duan / Min Jiao / Xiaoyu He / Qinyue Yu / Jiaxin Zhang / Qian Qin / Ruochen Wang / Fang Zheng / Peter M Hwang / Xiaoting Hua / Li Zhu / Yurong Wen /
Abstract: Multidrug-resistant Acinetobacter baumannii has emerged as one of the most antibiotic-resistant bacterial pathogens associated with nosocomial infection, with its resistance highly depending on ...Multidrug-resistant Acinetobacter baumannii has emerged as one of the most antibiotic-resistant bacterial pathogens associated with nosocomial infection, with its resistance highly depending on multiple multidrug efflux pumps. Here, we report the cryoelectron microscopy (cryo-EM) structure of Acinetobacter drug efflux G (AdeG), the inner membrane component of one of three important resistance-nodulation-cell division (RND) pump family members in A. baumannii, which is involved in drug resistance to chloramphenicol, trimethoprim, ciprofloxacin, and clindamycin. We systematically compare the structures and substrate binding specificities of AdeG, AdeB, and AdeJ multidrug efflux pumps via molecular docking, revealing potential determinants for drug binding. Knockout experiments demonstrate a functional complementarity between AdeABC, AdeFGH, and AdeIJK. Our study provides a structural understanding of A. baumannii multidrug efflux pump AdeG and reveals complementary drug efflux activity between AdeG and other RND efflux pumps, which may promote further rational drug discovery efforts targeting multidrug efflux pumps.
History
DepositionMar 20, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39532.png

Downloads & links

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Map

FileDownload / File: emd_39532.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.145
Minimum - Maximum-0.14895092 - 0.55124605
Average (Standard dev.)0.00021649289 (±0.012218236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39532_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39532_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Multidrug efflux RND transporter permease subunit AdeG

EntireName: Multidrug efflux RND transporter permease subunit AdeG
Components
  • Complex: Multidrug efflux RND transporter permease subunit AdeG
    • Protein or peptide: Cation/multidrug efflux pump
  • Ligand: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: Multidrug efflux RND transporter permease subunit AdeG

SupramoleculeName: Multidrug efflux RND transporter permease subunit AdeG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acinetobacter baumannii (bacteria)

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Macromolecule #1: Cation/multidrug efflux pump

MacromoleculeName: Cation/multidrug efflux pump / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 111.960359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NISKFFIDRP IFAGVLSVLI LLAGLLSVFQ LPISEYPEVV PPSVVVRAQY PGANPKVIAE TVASPLEESI NGVEDMLYMQ SQANSDGNL TITVNFKLGI DPDKAQQLVQ NRVSQAMPRL PEDVQRLGVT TLKSSPTLTM VVHLTSPDNR YDMTYLRNYA V LNVKDRLA ...String:
NISKFFIDRP IFAGVLSVLI LLAGLLSVFQ LPISEYPEVV PPSVVVRAQY PGANPKVIAE TVASPLEESI NGVEDMLYMQ SQANSDGNL TITVNFKLGI DPDKAQQLVQ NRVSQAMPRL PEDVQRLGVT TLKSSPTLTM VVHLTSPDNR YDMTYLRNYA V LNVKDRLA RLQGVGEVGL FGSGDYAMRV WLDPQKVAQR NLTATEIVNA IREQNIQVAA GTIGASPSNS PLQLSVNAQG RL TTEQEFA DIILKTAPDG AVTRLGDVAR VELAASQYGL RSLLDNKQAV AIPIFQAPGA NALQVSDQVR STMKELSKDF PSS IKYDIV YDPTQFVRAS IKAVVHTLLE AIALVVVVVI LFLQTWRASI IPLLAVPVSI IGTFALMLAF GYSINALSLF GMVL AIGIV VDDAIVVVEN VERNIEAGLN PREATYRAMR EVSGPIIAIA LTLVAVFVPL AFMTGLTGQF YKQFAMTIAI STVIS AFNS LTLSPALAAL LLKGHDAKPD ALTRIMNRVF GRFFALFNRV FSRASDRYSQ GVSRVISHKA SAMGVYAALL GLTVGI SYI VPGGFVPAQD KQYLISFAQL PNGASLDRTE AVIRKMSDTA LKQPGVESAV AFPGLSINGF TNSSSAGIVF VTLKPFD ER KAKDLSANAI AGALNQKYSA IQDAYIAVFP PPPVMGLGTM GGFKLQLEDR GALGYSALND AAQNFMKAAQ SAPELGPM F SSYQINVPQL NVDLDRVKAK QQGVAVTDVF NTMQIYLGSQ YVNDFNRFGR VYQVRAQADA PFRANPEDIL QLKTRNSAG QMVPLSSLVN VTQTYGPEMV VRYNGYTSAD INGGPAPGYS SSQAEAAVER IAAQTLPRGI KFEWTDLTYQ KILAGNAGLW VFPISVLLV FLVLAAQYES LTLPLAVILI VPMGILAALT GVWLTAGDNN IFTQIGLMVL VGLACKNAIL IVEFARELEM Q GATAFKAA VEASRLRLRP ILMTSIAFIM GVVPLVTSTG AGSEMRHAMG VAVFFGMIGV TFFGLFLTPA FYVLIRSLNS

UniProtKB: UNIPROTKB: A0AAQ1V714

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Macromolecule #2: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 6 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128482
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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