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- PDB-9gh6: CEACAM1 (35-234), focused refinement in the complex with CbpF -

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Entry
Database: PDB / ID: 9gh6
TitleCEACAM1 (35-234), focused refinement in the complex with CbpF
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 1
KeywordsCELL ADHESION / bacterial pathogenesis / adhesin / immunomodulation / host-pathogen interaction
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 / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / filamin binding ...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 / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / filamin binding / regulation of blood vessel remodeling / 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 / cell-cell adhesion via plasma-membrane adhesion molecules / negative regulation of interleukin-1 production / negative regulation of fatty acid biosynthetic process / positive regulation of vasculogenesis / 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 / microvillus membrane / bile acid and bile salt transport / transport vesicle membrane / blood vessel development / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / lateral plasma membrane / regulation of ERK1 and ERK2 cascade / specific granule membrane / regulation of cell migration / protein tyrosine kinase binding / basal plasma membrane / negative regulation of protein kinase activity / 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 junction / cell-cell junction / cell migration / actin binding / protein phosphatase binding / angiogenesis / 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 speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsMarongiu, G.L. / Fink, U. / Roderer, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Leibniz Association Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis for immune cell binding of via the trimeric autotransporter adhesin CbpF.
Authors: Gian Luca Marongiu / Uwe Fink / Felix Schöpf / Andreas Oder / Jens Peter von Kries / Daniel Roderer /
Abstract: (Fn), a commensal in the human oral cavity, is overrepresented in the colon microbiota of colorectal cancer (CRC) patients and is linked to tumor chemoresistance, metastasis, and a poor therapeutic ... (Fn), a commensal in the human oral cavity, is overrepresented in the colon microbiota of colorectal cancer (CRC) patients and is linked to tumor chemoresistance, metastasis, and a poor therapeutic prognosis. Fn produces numerous adhesins that mediate tumor colonization and downregulation of the host's antitumor immune response. One of these, the trimeric autotransporter adhesin (TAA) CEACAM binding protein of (CbpF), targets CEACAM1 on T-cells and has been associated with immune evasion of Fn-colonized tumors. Whereas the role of CEACAM1 in homophilic and heterophilic cell interactions and immune evasion is well described, the mechanistic details of its interaction with fusobacterial CbpF remain unknown due to the lack of a high-resolution structure of the adhesin-receptor complex. Here, we present two structures of CbpF alone and in complex with CEACAM1, obtained by cryogenic electron microscopy and single particle analysis. They reveal that CbpF forms a stable homotrimeric complex whose N-terminal part of the extracellular domain comprises a 64 Å long β roll domain with a unique lateral loop extension. CEACAM1 binds to this loop with high affinity via its N-terminal IgV-like domain with a nanomolar dissociation constant as determined by surface plasmon resonance. This study provides a comprehensive structural description of a fusobacterial TAA, illustrates a yet undescribed CEACAM1 binding mode, and paves the way for rational drug design targeting Fn in CRC.
History
DepositionAug 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Apr 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4718
Polymers47,9221
Non-polymers1,5487
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 Carcinoembryonic antigen-related cell adhesion molecule 1 / Biliary glycoprotein 1 / BGP-1


Mass: 47922.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: human CEACAM1 extracellular domain (Acro Biosystems), res. 35-234 are resolved
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM1, BGP, BGP1 / Production host: Homo sapiens (human) / References: UniProt: P13688
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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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: 1 CEACAM1 extracellular domain (35-234) in the context of the heterohexameric complex with CbpF
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.35 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6334
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.0particle selection
2EPU2.12image acquisition
4cryoSPARC4.4.0CTF correction
7Cootmodel fitting
9PHENIX1.21-5207model refinement
10cryoSPARC4.4.0initial Euler assignment
11cryoSPARC4.4.0final Euler assignment
12cryoSPARC4.4.0classification
13cryoSPARC4.4.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1766853
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 330202
Details: Map derived from shift of reconstruction center of full complex and masked refinement
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0021696
ELECTRON MICROSCOPYf_angle_d0.5592323
ELECTRON MICROSCOPYf_dihedral_angle_d6.303265
ELECTRON MICROSCOPYf_chiral_restr0.047285
ELECTRON MICROSCOPYf_plane_restr0.004300

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