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- EMDB-39900: Cryo-EM structure of outward state Anhydromuropeptide permease (A... -

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Basic information

Entry
Database: EMDB / ID: EMD-39900
TitleCryo-EM structure of outward state Anhydromuropeptide permease (AmpG) G50W/L269W
Map data
Sample
  • Complex: AmpG(G50W/L269W)_BRIL_Fab_nanobody complex(Apo)
    • Protein or peptide: Muropeptide transporter,Soluble cytochrome b562
    • Protein or peptide: anti-BRIL Fab Heavy chain
    • Protein or peptide: anti-BRIL Fab Nanobody
    • Protein or peptide: anti-BRIL Fab Light chain
Keywordstransporter / ampg / cryo-em / permease / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
AmpG-like permease/Acetyl-coenzyme A transporter 1 / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Cytochrome b562 / Cytochrome b562 / MFS transporter superfamily / Cytochrome c/b562
Similarity search - Domain/homology
Muropeptide transporter / Soluble cytochrome b562
Similarity search - Component
Biological speciesYokenella regensburgei (Enteric Group 45) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsYoo Y / Chang N / Kim U / Kim H / Cho H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of outward state Anhydromuropeptide permease (AmpG) G50W/L269W
Authors: Yoo Y / Chang N / Kim U / Kim H / Cho H
History
DepositionApr 26, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39900.png

Downloads & links

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Map

FileDownload / File: emd_39900.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 480 pix.
= 318.72 Å		0.66 Å/pix.
x 480 pix.
= 318.72 Å		0.66 Å/pix.
x 480 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4626034 - 0.7681111
Average (Standard dev.)-0.000053341275 (±0.010642612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39900_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39900_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: #1

Fileemd_39900_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 : AmpG(G50W/L269W)_BRIL_Fab_nanobody complex(Apo)

EntireName: AmpG(G50W/L269W)_BRIL_Fab_nanobody complex(Apo)
Components
  • Complex: AmpG(G50W/L269W)_BRIL_Fab_nanobody complex(Apo)
    • Protein or peptide: Muropeptide transporter,Soluble cytochrome b562
    • Protein or peptide: anti-BRIL Fab Heavy chain
    • Protein or peptide: anti-BRIL Fab Nanobody
    • Protein or peptide: anti-BRIL Fab Light chain

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Supramolecule #1: AmpG(G50W/L269W)_BRIL_Fab_nanobody complex(Apo)

SupramoleculeName: AmpG(G50W/L269W)_BRIL_Fab_nanobody complex(Apo) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Yokenella regensburgei (Enteric Group 45)
Molecular weightTheoretical: 124.8 kDa/nm

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Macromolecule #1: Muropeptide transporter,Soluble cytochrome b562

MacromoleculeName: Muropeptide transporter,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yokenella regensburgei (Enteric Group 45)
Molecular weightTheoretical: 63.770863 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PKSAILLILG FASGLPLALT SGTLQAWMTV ENIDLKTIWF FSLVGQAYVF KFLWSPVMDR YTPPFLGRRR GWLVTTQILL LIAIAAMGF LEPGTQLRWM AALAVVIAFC SASQDIVFDA WKTDVLPAEE RGTGAAISVL GYRLGMLVSG GLALWMADKW L GWQGMYWL ...String:
PKSAILLILG FASGLPLALT SGTLQAWMTV ENIDLKTIWF FSLVGQAYVF KFLWSPVMDR YTPPFLGRRR GWLVTTQILL LIAIAAMGF LEPGTQLRWM AALAVVIAFC SASQDIVFDA WKTDVLPAEE RGTGAAISVL GYRLGMLVSG GLALWMADKW L GWQGMYWL MAALLVPCII ATLLAPEPSA DLADNWETLN DNLKVIEKAD NAAQVKDALT KMRAAALDAQ KATPPKLEDK SP DSPEMKD FRHGFDILVG QIDDALKLAN EGKVKEAQAA AEQLKTTRNA YIQKYLGVPR TLEQAVVAPL RDFFGRNNAW LIL LLIVLY KLGDAFAMSL TTTFLIRGVG FDAGEVGMVN KTLGWIATII GALYGGVLMQ RLSLFRALLI FGILQGVSNA GYWL LSITD KHLMSMAVAV FFENLCGGMG TAAFVALLMT LCNKSFSATQ FALLSALSAV GRVYVGPIAG WFVEAHGWPT FYLFS VFAA VPGILLLLIC RKTLEYTQQT ESFMMRRHFS GAYQFALYLL LLGCLLLALW LIMLALNAID YTSFSFLAGL LEVAAL IAI AGVLLGAILD YLALRRTEE

UniProtKB: Muropeptide transporter, Soluble cytochrome b562, Muropeptide transporter

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Macromolecule #2: anti-BRIL Fab Heavy chain

MacromoleculeName: anti-BRIL Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.904656 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFNVV DFSLHWVRQA PGKGLEWVAY ISSSSGSTSY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARW GYWPGEPWWK AFDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFNVV DFSLHWVRQA PGKGLEWVAY ISSSSGSTSY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARW GYWPGEPWWK AFDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPK

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Macromolecule #3: anti-BRIL Fab Nanobody

MacromoleculeName: anti-BRIL Fab Nanobody / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.159438 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGRTIS RYAMSWFRQA PGKEREFVAV ARRSGDGAFY ADSVQGRFTV SRDDAKNTVY LQMNSLKPE DTAVYYCAID SDTFYSGSYD YWGQGTQVTV S

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Macromolecule #4: anti-BRIL Fab Light chain

MacromoleculeName: anti-BRIL Fab Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.20982 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNR

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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

Concentration11 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: 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: 0.2 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 236303
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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