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- EMDB-63958: Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-63958
TitleCryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM5
Map dataSharpen by DeepEMhancer
Sample
  • Complex: Fusobacterium nucleatum CbpF in complex with human CEACAM5
    • Protein or peptide: Fusobacterium nucleatum CbpF
    • Protein or peptide: Cell adhesion molecule CEACAM5
KeywordsFusobacterium nucleatum / trimeric autotransporter adhesin / CbpF / CEACAM5 / CELL ADHESION
Function / homology
Function and homology information


GPI anchor binding / homotypic cell-cell adhesion / negative regulation of myotube differentiation / Post-translational modification: synthesis of GPI-anchored proteins / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane ...GPI anchor binding / homotypic cell-cell adhesion / negative regulation of myotube differentiation / Post-translational modification: synthesis of GPI-anchored proteins / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane / apical plasma membrane / apoptotic process / negative regulation of apoptotic process / cell surface / protein homodimerization activity / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / 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 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 CEACAM5
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 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_63958.png

Downloads & links

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Map

FileDownload / File: emd_63958.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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Slices (1/2)

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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-0.0017969065 - 1.5467637
Average (Standard dev.)0.0011313839 (±0.023280492)
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_63958_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map before sharpening

Fileemd_63958_additional_1.map
AnnotationMap before sharpening
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-B map

Fileemd_63958_half_map_1.map
AnnotationHalf-B map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-A map

Fileemd_63958_half_map_2.map
AnnotationHalf-A 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 : Fusobacterium nucleatum CbpF in complex with human CEACAM5

EntireName: Fusobacterium nucleatum CbpF in complex with human CEACAM5
Components
  • Complex: Fusobacterium nucleatum CbpF in complex with human CEACAM5
    • Protein or peptide: Fusobacterium nucleatum CbpF
    • Protein or peptide: Cell adhesion molecule CEACAM5

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Supramolecule #1: Fusobacterium nucleatum CbpF in complex with human CEACAM5

SupramoleculeName: Fusobacterium nucleatum CbpF in complex with human CEACAM5
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 CEACAM5

MacromoleculeName: Cell adhesion molecule CEACAM5 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.404209 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKLTIESTPF NVAEGKEVLL LVHNLPQHLF GYSWYKGERV DGNRQIIGYV IGTQQATPGP AYSGREIIYP NASLLIQNII QNDTGFYTL HVIKSDLVNE EATGQFRVYP ELENLYFQGS AWSHPQFEKG GGSGGGSGGS AWSHPQFEK

UniProtKB: Cell adhesion molecule CEACAM5

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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: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 240256
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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