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- EMDB-47352: Cryo-EM structure of MdoD from Escherichia coli -

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Basic information

Entry
Database: EMDB / ID: EMD-47352
TitleCryo-EM structure of MdoD from Escherichia coli
Map datadeepemhanced map used for model refinement
Sample
  • Complex: MdoD dimer
    • Protein or peptide: Glucans biosynthesis protein D
KeywordsMdoD / signal peptide / glucanase / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


beta-glucan biosynthetic process / catalytic activity / outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
Glucan biosynthesis, MdoD / Glucan biosynthesis, periplasmic, MdoG C-terminal / Glucan biosynthesis protein MdoG/MdoD / Periplasmic glucan biosynthesis protein, MdoG / Glycoside hydrolase-type carbohydrate-binding / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Galactose mutarotase-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Glucans biosynthesis protein D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsDeme JC / Bryant OJ / Berks BC / Lea SM
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L000776/1 United Kingdom
Wellcome Trust107929/Z/15/Z United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To Be Published
Title: Structure of the twin-arginine protein translocation pathway core complex and the molecular basis for substrate recognition
Authors: Deme JC / Bryant OJ / Berks BC / Lea SM
History
DepositionOct 17, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47352.png

Downloads & links

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Map

FileDownload / File: emd_47352.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdeepemhanced map used for model refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 512 pix.
= 354.816 Å		0.69 Å/pix.
x 512 pix.
= 354.816 Å		0.69 Å/pix.
x 512 pix.
= 354.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.693 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017563532 - 1.4870654
Average (Standard dev.)0.00029847864 (±0.0119909905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 354.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47352_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Mask used for FSC calculation

Fileemd_47352_additional_1.map
AnnotationMask used for FSC calculation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: B-factor sharpened map

Fileemd_47352_additional_2.map
AnnotationB-factor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_47352_additional_3.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_47352_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_47352_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MdoD dimer

EntireName: MdoD dimer
Components
  • Complex: MdoD dimer
    • Protein or peptide: Glucans biosynthesis protein D

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Supramolecule #1: MdoD dimer

SupramoleculeName: MdoD dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Glucans biosynthesis protein D

MacromoleculeName: Glucans biosynthesis protein D / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 62.916844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMDRRRFIKG SMAMAAVCGT SGIASLFSQA AFAADSDIAD GQTQRFDFSI LQSMAHDLAQ TAWRGAPRPL PDTLATMTPQ AYNSIQYDA EKSLWHNVEN RQLDAQFFHM GMGFRRRVRM FSVDPATHLA REIHFRPELF KYNDAGVDTK QLEGQSDLGF A GFRVFKAP ...String:
SMDRRRFIKG SMAMAAVCGT SGIASLFSQA AFAADSDIAD GQTQRFDFSI LQSMAHDLAQ TAWRGAPRPL PDTLATMTPQ AYNSIQYDA EKSLWHNVEN RQLDAQFFHM GMGFRRRVRM FSVDPATHLA REIHFRPELF KYNDAGVDTK QLEGQSDLGF A GFRVFKAP ELARRDVVSF LGASYFRAVD DTYQYGLSAR GLAIDTYTDS KEEFPDFTAF WFDTVKPGAT TFTVYALLDS AS ITGAYKF TIHCEKSQVI MDVENHLYAR KDIKQLGIAP MTSMFSCGTN ERRMCDTIHP QIHDSDRLSM WRGNGEWICR PLN NPQKLQ FNAYTDNNPK GFGLLQLDRD FSHYQDIMGW YNKRPSLWVE PRNKWGKGTI GLMEIPTTGE TLDNIVCFWQ PEKA VKAGD EFAFQYRLYW SAQPPVHCPL ARVMATRTGM GGFSEGWAPG EHYPEKWARR FAVDFVGGDL KAAAPKGIEP VITLS SGEA KQIEILYIEP IDGYRIQFDW YPTSDSTDPV DMRMYLRCQG DAISETWLYQ YFPPAPDKRQ YVDDRVMS

UniProtKB: Glucans biosynthesis protein D

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 52.1 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 770564
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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