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- EMDB-51348: CEACAM1 (35-234), focused refinement in the complex with CbpF -

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Basic information

Entry
Database: EMDB / ID: EMD-51348
TitleCEACAM1 (35-234), focused refinement in the complex with CbpF
Map dataMain map, sharpened with DeepEMhancer
Sample
  • Complex: 1 CEACAM1 extracellular domain (35-234) in the context of the heterohexameric complex with CbpF
    • Protein or peptide: Carcinoembryonic antigen-related cell adhesion molecule 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsbacterial pathogenesis / adhesin / immunomodulation / host-pathogen interaction / 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 / 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 / bile acid and bile salt transport / microvillus membrane / 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 / protein tyrosine kinase binding / regulation of cell migration / 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 migration / cell-cell junction / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMarongiu GL / Fink U / Roderer D
Funding support Germany, 1 items
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, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51348.png

Downloads & links

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Map

FileDownload / File: emd_51348.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, sharpened with DeepEMhancer
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.119
Minimum - Maximum-0.019739397 - 1.6016871
Average (Standard dev.)0.0011177342 (±0.02268691)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51348_msk_1.map
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Additional map: Non-sharpened map

Fileemd_51348_additional_1.map
AnnotationNon-sharpened map
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Half map: #1

Fileemd_51348_half_map_1.map
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Half map: #2

Fileemd_51348_half_map_2.map
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Sample components

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Entire : 1 CEACAM1 extracellular domain (35-234) in the context of the het...

EntireName: 1 CEACAM1 extracellular domain (35-234) in the context of the heterohexameric complex with CbpF
Components
  • Complex: 1 CEACAM1 extracellular domain (35-234) in the context of the heterohexameric complex with CbpF
    • Protein or peptide: Carcinoembryonic antigen-related cell adhesion molecule 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 1 CEACAM1 extracellular domain (35-234) in the context of the het...

SupramoleculeName: 1 CEACAM1 extracellular domain (35-234) in the context of the heterohexameric complex with CbpF
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Carcinoembryonic antigen-related cell adhesion molecule 1

MacromoleculeName: Carcinoembryonic antigen-related cell adhesion molecule 1
type: protein_or_peptide / ID: 1
Details: human CEACAM1 extracellular domain (Acro Biosystems), res. 35-234 are resolved
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.922082 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGHLSAPLHR VRVPWQGLLL TASLLTFWNP PTTAQLTTES MPFNVAEGKE VLLLVHNLPQ QLFGYSWYKG ERVDGNRQIV GYAIGTQQA TPGPANSGRE TIYPNASLLI QNVTQNDTGF YTLQVIKSDL VNEEATGQFH VYPELPKPSI SSNNSNPVED K DAVAFTCE ...String:
MGHLSAPLHR VRVPWQGLLL TASLLTFWNP PTTAQLTTES MPFNVAEGKE VLLLVHNLPQ QLFGYSWYKG ERVDGNRQIV GYAIGTQQA TPGPANSGRE TIYPNASLLI QNVTQNDTGF YTLQVIKSDL VNEEATGQFH VYPELPKPSI SSNNSNPVED K DAVAFTCE PETQDTTYLW WINNQSLPVS PRLQLSNGNR TLTLLSVTRN DTGPYECEIQ NPVSANRSDP VTLNVTYGPD TP TISPSDT YYRPGANLSL SCYAASNPPA QYSWLINGTF QQSTQELFIP NITVNNSGSY TCHANNSVTG CNRTTVKTII VTE LSPVVA KPQIKASKTT VTGDKDSVNL TCSTNDTGIS IRWFFKNQSL PSSERMKLSQ GNTTLSINPV KREDAGTYWC EVFN PISKN QSDPIMLNVN YNALPQENGL SPGHHHHHH

UniProtKB: Cell adhesion molecule CEACAM1

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6334 / Average electron dose: 52.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1766853
Startup modelType of model: OTHER
Details: Map derived from shift of reconstruction center and masked refinement
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0)
Details: Map derived from shift of reconstruction center of full complex and masked refinement
Number images used: 330202
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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