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- EMDB-60190: Cryo-EM structure of inward-facing Anhydromuropeptide permease (A... -

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Basic information

Entry
Database: EMDB / ID: EMD-60190
TitleCryo-EM structure of inward-facing Anhydromuropeptide permease (AmpG) in complex with GlcNAc-1,6-anhMurNAc
Map data
Sample
  • Complex: Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex with GlcNAc-1,6-anhMurNAc
    • Protein or peptide: Muropeptide transporter
  • Ligand: (2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid
KeywordsAmpG / MFS / Anhydromuropeptide permease / MEMBRANE PROTEIN
Function / homologyAmpG-like permease/Acetyl-coenzyme A transporter 1 / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Muropeptide transporter
Function and homology information
Biological speciesYokenella regensburgei (Enteric Group 45)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsChang N / Kim U / Yoo Y / Kim H / Cho H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of inward-facing Anhydromuropeptide permease (AmpG) in complex with GlcNAc-1,6-anhMurNAc
Authors: Chang N / Kim U / Kim H / Yoo Y / Cho H
History
DepositionMay 16, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60190.png

Downloads & links

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Map

FileDownload / File: emd_60190.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 336 pix.
= 284.928 Å		0.85 Å/pix.
x 336 pix.
= 284.928 Å		0.85 Å/pix.
x 336 pix.
= 284.928 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.8948712 - 0.90786177
Average (Standard dev.)0.00044959714 (±0.010671194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 284.928 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60190_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_60190_half_map_1.map
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Half map: #1

Fileemd_60190_half_map_2.map
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Sample components

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Entire : Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex wi...

EntireName: Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex with GlcNAc-1,6-anhMurNAc
Components
  • Complex: Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex with GlcNAc-1,6-anhMurNAc
    • Protein or peptide: Muropeptide transporter
  • Ligand: (2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid

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Supramolecule #1: Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex wi...

SupramoleculeName: Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex with GlcNAc-1,6-anhMurNAc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Yokenella regensburgei (Enteric Group 45)

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Macromolecule #1: Muropeptide transporter

MacromoleculeName: Muropeptide transporter / 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 BL21(DE3) (bacteria)
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: Muropeptide transporter

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Macromolecule #2: (2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-aceta...

MacromoleculeName: (2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: 2YP
Molecular weightTheoretical: 478.448 Da
Chemical component information

ChemComp-2YP:
(2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid

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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

Concentration9 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
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: 67.0 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133506
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC

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