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- EMDB-60093: Cryo-EM structure of inward state Anhydromuropeptide permease (AmpG) -

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Basic information

Entry
Database: EMDB / ID: EMD-60093
TitleCryo-EM structure of inward state Anhydromuropeptide permease (AmpG)
Map data
Sample
  • Complex: AmpG, Anhydromuropeptide permease
    • Protein or peptide: Protein AmpG
Keywordsantibiotic resistance / membrane transporter / TRANSPORT PROTEIN
Function / homology:
Function and homology information
Biological speciesYokenella regensburgei (Enteric Group 45)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsCho HS / Kim U / Chang N / Kim H / Yoo Y
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nat Commun / Year: 2025
Title: Structural and functional insights of AmpG in muropeptide transport and multiple β-lactam antibiotics resistance.
Authors: Nienping Chang / Hoyoung Kim / Uijin Kim / Yongju Cho / Youngki Yoo / Hyunsook Lee / Ji Won Kim / Min Sung Kim / Jaeho Lee / Young-Lag Cho / Kitae Kim / Dongeun Yong / Hyun-Soo Cho /
Abstract: Anhydromuropeptide permease (AmpG) is a transporter protein located in the inner membrane of certain gram -negative bacteria, involved in peptidoglycan (PG) recycling and β-lactamase induction. ...Anhydromuropeptide permease (AmpG) is a transporter protein located in the inner membrane of certain gram -negative bacteria, involved in peptidoglycan (PG) recycling and β-lactamase induction. Decreased AmpG function reduces resistance of antibiotic-resistant bacteria to β-lactam antibiotics. Therefore, AmpG-targeting inhibitors are promising 'antibiotic adjuvants'. However, as the tertiary structure of AmpG has not yet been identified, the development of targeted inhibitors remains challenging. We present four cryo-electron microscopy (cryo-EM) structures: the apo-inward and apo-outward state structures and the inward-occluded and outward states complexed with the substrate GlcNAc-1,6-anhMurNAc. Through functional analysis and molecular dynamics (MD) simulations, we identified motif A, which stabilizes the outward state, substrate-binding pocket, and protonation-related residues. Based on the structure of AmpG and our experimental results, we propose a muropeptide transport mechanism for AmpG. A deeper understanding of its structure and transport mechanism provides a foundation for the development of antibiotic adjuvants.
History
DepositionMay 10, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60093.png

Downloads & links

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Map

FileDownload / File: emd_60093.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 320 pix.
= 288.416 Å		0.9 Å/pix.
x 320 pix.
= 288.416 Å		0.9 Å/pix.
x 320 pix.
= 288.416 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9013 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.0607773 - 1.369571
Average (Standard dev.)0.0006474201 (±0.023115167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 288.41602 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60093_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_60093_half_map_2.map
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Sample components

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Entire : AmpG, Anhydromuropeptide permease

EntireName: AmpG, Anhydromuropeptide permease
Components
  • Complex: AmpG, Anhydromuropeptide permease
    • Protein or peptide: Protein AmpG

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Supramolecule #1: AmpG, Anhydromuropeptide permease

SupramoleculeName: AmpG, Anhydromuropeptide permease / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Yokenella regensburgei (Enteric Group 45)

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Macromolecule #1: Protein AmpG

MacromoleculeName: Protein AmpG / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yokenella regensburgei (Enteric Group 45)
Molecular weightTheoretical: 54.069086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANHYLRIFQ QPKSAILLIL GFASGLPLAL TSGTLQAWMT VENIDLKTIG FFSLVGQAYV FKFLWSPVMD RYTPPFLGRR RGWLVTTQI LLLIAIAAMG FLEPGTQLRW MAALAVVIAF CSASQDIVFD AWKTDVLPAE ERGTGAAISV LGYRLGMLVS G GLALWMAD ...String:
MANHYLRIFQ QPKSAILLIL GFASGLPLAL TSGTLQAWMT VENIDLKTIG FFSLVGQAYV FKFLWSPVMD RYTPPFLGRR RGWLVTTQI LLLIAIAAMG FLEPGTQLRW MAALAVVIAF CSASQDIVFD AWKTDVLPAE ERGTGAAISV LGYRLGMLVS G GLALWMAD KWLGWQGMYW LMAALLVPCI IATLLAPEPS DVVPVPRTLE QAVVAPLRDF FGRNNAWLIL LLIVLYKLGD AF AMSLTTT FLIRGVGFDA GEVGMVNKTL GLIATIIGAL YGGVLMQRLS LFRALLIFGI LQGVSNAGYW LLSITDKHLM SMA VAVFFE NLCGGMGTAA FVALLMTLCN KSFSATQFAL LSALSAVGRV YVGPIAGWFV EAHGWPTFYL FSVFAAVPGI LLLL ICRKT LEYTQQTESF MMRRHFSGAY QFALYLLLLG CLLLALWLIM LALNAIDYTS FSFLAGLLEV AALIAIAGVL LGAIL DYLA LRRTEEHKLA

UniProtKB: UNIPROTKB: G9Z488

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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 mg/mL
BufferpH: 7.5
GridModel: Quantifoil / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86432
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 54.1
Output model

PDB-8zgz:
Cryo-EM structure of inward state Anhydromuropeptide permease (AmpG)

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