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- EMDB-67697: E coli CNF1 in complex with BCAM receptor -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-67697
TitleE coli CNF1 in complex with BCAM receptor
Map data
Sample
  • Complex: E coli CNF1 toxin in complex with BCAM receptor
    • Complex: BCAM receptor
      • Protein or peptide: Basal cell adhesion molecule
    • Complex: E coli CNF1 Toxin
      • Protein or peptide: Cytotoxic necrotizing factor 1
KeywordsE coli CNF1 toxin / BCAM receptor / TOXIN
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell-cell junction / laminin receptor activity / cell-matrix adhesion / laminin binding / angiogenesis / transmembrane signaling receptor activity / cell adhesion / extracellular matrix / : / external side of plasma membrane ...symbiont-mediated perturbation of host cell-cell junction / laminin receptor activity / cell-matrix adhesion / laminin binding / angiogenesis / transmembrane signaling receptor activity / cell adhesion / extracellular matrix / : / external side of plasma membrane / signal transduction / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Cytotoxic necrotizing factor, Rho-activating domain / Domain of unknown function DUF4765 / Cytotoxic necrotizing factor, Rho-activating domain superfamily / Rho-activating domain of cytotoxic necrotizing factor / Domain of unknown function (DUF4765) / Domain of unknown function DUF6543 / Dermonecrotic toxin, N-terminal domain / Cytotoxic necrotizing factor-like, catalytic / : / CD80-like, immunoglobulin C2-set ...Cytotoxic necrotizing factor, Rho-activating domain / Domain of unknown function DUF4765 / Cytotoxic necrotizing factor, Rho-activating domain superfamily / Rho-activating domain of cytotoxic necrotizing factor / Domain of unknown function (DUF4765) / Domain of unknown function DUF6543 / Dermonecrotic toxin, N-terminal domain / Cytotoxic necrotizing factor-like, catalytic / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Basal cell adhesion molecule / Cytotoxic necrotizing factor 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsZhou C / Zheng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: E coli CNF1 in complex with BCAM receptor
Authors: Zhou C / Zheng Y
History
DepositionDec 14, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67697.png

Downloads & links

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Map

FileDownload / File: emd_67697.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-2.086287 - 2.7737951
Average (Standard dev.)-0.00012179466 (±0.04813704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67697_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67697_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 : E coli CNF1 toxin in complex with BCAM receptor

EntireName: E coli CNF1 toxin in complex with BCAM receptor
Components
  • Complex: E coli CNF1 toxin in complex with BCAM receptor
    • Complex: BCAM receptor
      • Protein or peptide: Basal cell adhesion molecule
    • Complex: E coli CNF1 Toxin
      • Protein or peptide: Cytotoxic necrotizing factor 1

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Supramolecule #1: E coli CNF1 toxin in complex with BCAM receptor

SupramoleculeName: E coli CNF1 toxin in complex with BCAM receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 110 KDa

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Supramolecule #2: BCAM receptor

SupramoleculeName: BCAM receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: E coli CNF1 Toxin

SupramoleculeName: E coli CNF1 Toxin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Basal cell adhesion molecule

MacromoleculeName: Basal cell adhesion molecule / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.74409 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: AEVRLSVPPL VEVMRGKSVI LDCTPTGTHD HYMLEWFLTD RSGARPRLAS AEMQGSELQV TMHDTRGRSP PYQLDSQGRL VLAEAQVGD ERDYVCVVRA GAAGTAEATA RLNVFAKPEA TEVSPNKGTL SVMEDSAQEI ATCNSRNGNP APKITWYRNG Q RLEVPVEM ...String:
AEVRLSVPPL VEVMRGKSVI LDCTPTGTHD HYMLEWFLTD RSGARPRLAS AEMQGSELQV TMHDTRGRSP PYQLDSQGRL VLAEAQVGD ERDYVCVVRA GAAGTAEATA RLNVFAKPEA TEVSPNKGTL SVMEDSAQEI ATCNSRNGNP APKITWYRNG Q RLEVPVEM NPEGYMTSRT VREASGLLSL TSTLYLRLRK DDRDASFHCA AHYSLPEGRH GRLDSPTFHL TLHYPTEHVQ FW VGSPSTP AGWVREGDTV QLLCRGDGSP SPEYTLFRLQ DEQEEVLNVN LEGNLTLEGV TRGQSGTYGC RVEDYDAADD VQL SKTLEL RVAYLDPLEL SEGKVLSLPL NSSAVVNCSV HGLPTPALRW TKDSTPLGDG PMLSLSSITF DSNGTYVCEA SLPT VPVLS RTQNFTLLVQ GSPELKTAEI EPKADGSWRE GDEVTLICSA RGHPDPKLSW SQLGGSPAEP IPGRQGWVSS SLTLK VTSA LSRDGISCEA SNPHGNKRHV FHFGTVS

UniProtKB: Basal cell adhesion molecule

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Macromolecule #2: Cytotoxic necrotizing factor 1

MacromoleculeName: Cytotoxic necrotizing factor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 114.000633 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGNQWQQKYL LEYNELVSNF PSPERVVSDY IKNCFKTDLP WFSRIDPDNA YFICFSQNRS NSRSYTGWDH LGKYKTEVLT LTQAALINI GYRFDVFDDA NSSTGIYKTK SADVFNEENE EKMLPSEYLH FLQKCDFAGV YGKTLSDYWS KYYDKFKLLL K NYYISSAL ...String:
MGNQWQQKYL LEYNELVSNF PSPERVVSDY IKNCFKTDLP WFSRIDPDNA YFICFSQNRS NSRSYTGWDH LGKYKTEVLT LTQAALINI GYRFDVFDDA NSSTGIYKTK SADVFNEENE EKMLPSEYLH FLQKCDFAGV YGKTLSDYWS KYYDKFKLLL K NYYISSAL YLYKNGELDE REYNFSMNAL NRSDNISLLF FDIYGYYASD IFVAKNNDKV MLFIPGAKKP FLFKKNIADL RL TLKELIK DSDKQQLLSQ HFSLYSRQDG VSYAGVNSVL HAIENDGNFN ESYFLYSNKT LSNKDVFDAI AISVKKRSFS DGD IVIKSN SEAQRDYALT ILQTILSMTP IFDIVVPEVS VPLGLGIITS SMGISFDQLI NGDTYEERRS AIPGLATNAV LLGL SFAIP LLISKAGINQ EVLSSVINNE GRTLNETNID IFLKEYGIAE DSISSTNLLD VKLKSSGQHV NIVKLSDEDN QIVAV KGSS LSGIYYEVDI ETGYEILSRR IYRTEYNNEI LWTRGGGLKG GQPFDFESLN IPVFFKDEPY SAVTGSPLSF INDDSS LLY PDTNPKLPQP TSEMDIVNYV KGSGSFGDRF VTLMRGATEE EAWNIASYHT AGGSTEELHE ILLGQGPQSS LGFTEYT SN VNSADAASRR HFLVVIKVHV KYITNNNVSY VNHWAIPDEA PVEVLAVVDR RFNFPEPSTP PDISTIRKLL SLRYFKES I ESTSKSNFQK LSRGNIDVLK GRGSISSTRQ RAIYPYFEAA NADEQQPLFF YIKKDRFDNH GYDQYFYDNT VGLNGIPTL NTYTGEIPSD SSSLGSTYWK KYNLTNETSI IRVSNSARGA NGIKIALEEV QEGKPVIITS GNLSGCTTIV ARKEGYIYKV HTGTTKSLA GFTSTTGVKK AVEVLELLTK EPIPRVEGIM SNDFLVDYLS ENFEDSLITY SSSEKKPDSQ ITIIRDNVSV F PYFLDNIP EHGFGTSATV LVRVDGNVVV RSLSESYSLN ADASEISVLK VFSKKF

UniProtKB: Cytotoxic necrotizing factor 1

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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

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6532331 / Details: Autopick
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 560395
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7) / Details: Ab initio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7) / Details: Non uniform refinement

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