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- EMDB-73868: Constituent EM map: local refinement of putative MUC2 binding dom... -

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Basic information

Entry
Database: EMDB / ID: EMD-73868
TitleConstituent EM map: local refinement of putative MUC2 binding domain of rEatAp and Fab G12 from best Fab-containing 2D classes
Map datalocal refinement 2; sharpened map (resampled onto consensus map)
Sample
  • Complex: Binary complex of the recombinant EatA passenger domain with Fab G12
    • Complex: Enterotoxigenic Escherichia coli autotransporter A (EatA) passenger domain
    • Complex: Fragment antigen binding domain of monoclonal antibody G12
KeywordsPROTEASE / BETA-HELIX / SECRETED / MONOCLONAL ANTIBODY / HYDROLASE / HYDROLASE-IMMUNE SYSTEM complex
Biological speciesEscherichia coli (E. coli) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsBuckley DP / Berndsen ZT
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089894 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI126887 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007172 United States
Department of Veterans Affairs (VA, United States)5I01BX001469-05 United States
CitationJournal: To Be Published
Title: Human infection with enterotoxigenic E. coli elicits antibodies that broadly neutralize mucin-degrading proteases of pathogenic E. coli and Shigella
Authors: Buckley DP / Akhtar M / Thapa M / Schmitz A / Turner J / Vickers TJ / Khatoon N / Kaisar H / Coggin JA / Ganguli D / Sheikh A / Laird RM / Poly F / Porter CK / Baboo S / Ruiz-Perez F / ...Authors: Buckley DP / Akhtar M / Thapa M / Schmitz A / Turner J / Vickers TJ / Khatoon N / Kaisar H / Coggin JA / Ganguli D / Sheikh A / Laird RM / Poly F / Porter CK / Baboo S / Ruiz-Perez F / Nataro JP / Miller MJ / Bhuiyan TR / Qadri F / Trillo-Muyo S / Dolan B / van der Post S / Ellebedy A / Berndsen ZT / Fleckenstein JM
History
DepositionNov 16, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73868.png

Downloads & links

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Map

FileDownload / File: emd_73868.map.gz / Format: CCP4 / Size: 172.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refinement 2; sharpened map (resampled onto consensus map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 356 pix.
= 306.16 Å		0.86 Å/pix.
x 356 pix.
= 306.16 Å		0.86 Å/pix.
x 356 pix.
= 306.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.229
Minimum - Maximum-1.0405526 - 1.5656327
Average (Standard dev.)-0.000095249765 (±0.017491419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions356356356
Spacing356356356
CellA=B=C: 306.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: local refinement 2; half map A (resampled onto consensus map)

Fileemd_73868_half_map_1.map
Annotationlocal refinement 2; half map A (resampled onto consensus map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: local refinement 2; half map B (resampled onto consensus map)

Fileemd_73868_half_map_2.map
Annotationlocal refinement 2; half map B (resampled onto consensus 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 : Binary complex of the recombinant EatA passenger domain with Fab G12

EntireName: Binary complex of the recombinant EatA passenger domain with Fab G12
Components
  • Complex: Binary complex of the recombinant EatA passenger domain with Fab G12
    • Complex: Enterotoxigenic Escherichia coli autotransporter A (EatA) passenger domain
    • Complex: Fragment antigen binding domain of monoclonal antibody G12

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Supramolecule #1: Binary complex of the recombinant EatA passenger domain with Fab G12

SupramoleculeName: Binary complex of the recombinant EatA passenger domain with Fab G12
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli) / Strain: H10407
Molecular weightTheoretical: 23 KDa

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Supramolecule #2: Enterotoxigenic Escherichia coli autotransporter A (EatA) passeng...

SupramoleculeName: Enterotoxigenic Escherichia coli autotransporter A (EatA) passenger domain
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Mature, secreted EatA passenger domain (cleaved N-terminal signal peptide and C-terminal beta-barrel regions) from recombinant expression of full-length EatA
Source (natural)Organism: Escherichia coli (E. coli) / Strain: H10407

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Supramolecule #3: Fragment antigen binding domain of monoclonal antibody G12

SupramoleculeName: Fragment antigen binding domain of monoclonal antibody G12
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Details: Fab fragment generated from papain-digested monoclonal G12 IgG
Source (natural)Organism: Homo sapiens (human)

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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

Concentration0.7 mg/mL
BufferpH: 7.4 / Component - Concentration: 1.0 X / Component - Formula: TBS / Component - Name: Tris-Buffered Saline
Details: 10X TBS: 250mM Tris, 27mM potassium chloride, 1.37M sodium chloride, pH 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Added 1X Lauryl Maltose Neopentyl Glycol (LMNG) detergent to sample prior to vitrification..
DetailsThis sample displayed heterogeneity in the ice, resulting in preferred orientation in the final map.

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 87.15 K / Max: 87.15 K
SoftwareName: SerialEM (ver. 4)
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 2 / Number real images: 6382 / Average exposure time: 2.1 sec. / Average electron dose: 49.0 e/Å2
Details: Movies collected during first session: 1972 Movies collected during second session: 4410
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1244157
Details: Initial particle set was obtained by CryoSegNet AI picking, followed by cryoSPARC 2D classification to redo particle picking with 2D templates
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AB-INITIO
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 146838
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.8)
DetailsRigid body fitting of AlphaFold-derived models was done in ChimeraX, followed by multiple rounds of local fitting in Coot and Phenix real-space refinement
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient

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