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- EMDB-63959: Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-63959
TitleCryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM1
Map dataSharpen by DeepEMhancer
Sample
  • Complex: Fusobacterium nucleatum CbpF in complex with human CEACAM1
    • Protein or peptide: Fusobacterium nucleatum CbpF
    • Protein or peptide: Cell adhesion molecule CEACAM1
KeywordsFusobacterium nucleatum / trimeric autotransporter adhesin / CbpF / CEACAM1 / CELL ADHESION
Function / homology
Function and homology information


regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / Regulation of MITF-M dependent genes involved in invasion / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / negative regulation of hepatocyte proliferation / filamin binding / regulation of epidermal growth factor receptor signaling pathway / regulation of blood vessel remodeling ...regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / Regulation of MITF-M dependent genes involved in invasion / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / negative regulation of hepatocyte proliferation / filamin binding / regulation of epidermal growth factor receptor signaling pathway / regulation of blood vessel remodeling / regulation of sprouting angiogenesis / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of lipid biosynthetic process / negative regulation of T cell mediated cytotoxicity / regulation of endothelial cell migration / negative regulation of granulocyte differentiation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin catabolic process / Fibronectin matrix formation / common myeloid progenitor cell proliferation / : / negative regulation of interleukin-1 production / positive regulation of vasculogenesis / negative regulation of fatty acid biosynthetic process / negative regulation of platelet aggregation / bile acid transmembrane transporter activity / negative regulation of vascular permeability / regulation of immune system process / wound healing, spreading of cells / negative regulation of T cell receptor signaling pathway / bile acid and bile salt transport / transport vesicle membrane / blood vessel development / microvillus membrane / homophilic cell-cell adhesion / tertiary granule membrane / lateral plasma membrane / regulation of ERK1 and ERK2 cascade / specific granule membrane / negative regulation of protein kinase activity / basal plasma membrane / regulation of cell migration / protein tyrosine kinase binding / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / adherens junction / regulation of cell growth / kinase binding / cellular response to insulin stimulus / cell-cell junction / cell junction / cell migration / actin binding / angiogenesis / protein phosphatase binding / calmodulin binding / protein dimerization activity / cell adhesion / apical plasma membrane / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...: / Immunoglobulin domain / Immunoglobulin / 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
Cell adhesion molecule CEACAM1
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.11 Å
AuthorsLi LJ / Shen F / Zhao X / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis of Fusobacterium nucleatum CbpF binding to human CEACAM1 and CEACAM5
Authors: Shen F / Li LJ / Zhao X / Gao GF
History
DepositionMar 27, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63959.png

Downloads & links

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Map

FileDownload / File: emd_63959.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpen by DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 320 pix.
= 243.2 Å		0.76 Å/pix.
x 320 pix.
= 243.2 Å		0.76 Å/pix.
x 320 pix.
= 243.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.0017590832 - 1.8480554
Average (Standard dev.)0.0011608448 (±0.024186818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63959_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: Map before sharpening

Fileemd_63959_additional_1.map
AnnotationMap before sharpening
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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-A map

Fileemd_63959_half_map_1.map
AnnotationHalf-A map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-B map

Fileemd_63959_half_map_2.map
AnnotationHalf-B map
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Sample components

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Entire : Fusobacterium nucleatum CbpF in complex with human CEACAM1

EntireName: Fusobacterium nucleatum CbpF in complex with human CEACAM1
Components
  • Complex: Fusobacterium nucleatum CbpF in complex with human CEACAM1
    • Protein or peptide: Fusobacterium nucleatum CbpF
    • Protein or peptide: Cell adhesion molecule CEACAM1

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Supramolecule #1: Fusobacterium nucleatum CbpF in complex with human CEACAM1

SupramoleculeName: Fusobacterium nucleatum CbpF in complex with human CEACAM1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Fusobacterium nucleatum (bacteria)

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Macromolecule #1: Fusobacterium nucleatum CbpF

MacromoleculeName: Fusobacterium nucleatum CbpF / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 35.874555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVSFSAPVFQ AGTGTDSTVA GVNNEANGEK SSAFGYENKA KEKLSSAFGY KNIANGIEGS AFGISNLAKG QYSSAFGFRN VANKRHSSA FGSGNEANGE QSSAFGFKNT VSGFNSSAFG SQYEVTGNFS GAFGMGEFNG QYQYKNEGNN SYMIGNKNKI A SGSNDNFI ...String:
MVSFSAPVFQ AGTGTDSTVA GVNNEANGEK SSAFGYENKA KEKLSSAFGY KNIANGIEGS AFGISNLAKG QYSSAFGFRN VANKRHSSA FGSGNEANGE QSSAFGFKNT VSGFNSSAFG SQYEVTGNFS GAFGMGEFNG QYQYKNEGNN SYMIGNKNKI A SGSNDNFI LGNNVHIGGG INNSVALGNN STVSASNTVS VGSSTLKRKI VNVGDGAISA NSSDAVTGRQ LYSGNGIDTA AW QNKLNVT RKNDYKDAND IDVNKWKAKL GVGSGGGGGT ADIENLRNEV NEKIDDVKDE VRENLYFQGS AWSHPQFEKG GGS GGGSGG SAWSHPQFEK HHHHHH

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Macromolecule #2: Cell adhesion molecule CEACAM1

MacromoleculeName: Cell adhesion molecule CEACAM1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.913442 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQLTTESMPF NVAEGKEVLL LVHNLPQQLF GYSWYKGERV DGNRQIVGYA IGTQQATPGP ANSGRETIYP NASLLIQNVT QNDTGFYTL QVIKSDLVNE EATGQFHVYE NLYFQGSAWS HPQFEKGGGS GGGSGGSAWS HPQFEK

UniProtKB: Cell adhesion molecule CEACAM1

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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: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 430775
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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