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- PDB-9u93: Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with... -

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Basic information

Entry
Database: PDB / ID: 9u93
TitleCryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM5
Components
  • Cell adhesion molecule CEACAM5
  • Fusobacterium nucleatum CbpF
KeywordsCELL ADHESION / Fusobacterium nucleatum / trimeric autotransporter adhesin / CbpF / CEACAM5
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLi, L.J. / Shen, F. / Zhao, X. / Gao, G.F.
Funding support China, 1items
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, L.J. / Zhao, X. / Gao, G.F.
History
DepositionMar 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Fusobacterium nucleatum CbpF
F: Cell adhesion molecule CEACAM5
B: Fusobacterium nucleatum CbpF
D: Cell adhesion molecule CEACAM5
A: Fusobacterium nucleatum CbpF
E: Cell adhesion molecule CEACAM5


Theoretical massNumber of molelcules
Total (without water)156,8366
Polymers156,8366
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Fusobacterium nucleatum CbpF


Mass: 35874.555 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein Cell adhesion molecule CEACAM5 / Carcinoembryonic antigen / CEA / Carcinoembryonic antigen-related cell adhesion molecule 5 / CEA ...Carcinoembryonic antigen / CEA / Carcinoembryonic antigen-related cell adhesion molecule 5 / CEA cell adhesion molecule 5 / Meconium antigen 100


Mass: 16404.209 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM5, CEA / Production host: Escherichia coli (E. coli) / References: UniProt: P06731
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Fusobacterium nucleatum CbpF in complex with human CEACAM5
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 240256 / Symmetry type: POINT
RefinementHighest resolution: 2.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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