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- EMDB-51347: Complex of Fusobacterium nucleatum CbpF with human CEACAM1 -

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Basic information

Entry
Database: EMDB / ID: EMD-51347
TitleComplex of Fusobacterium nucleatum CbpF with human CEACAM1
Map dataFull map, sharpened with DeepEMhancer
Sample
  • Complex: Hetero-hexameric complex of CbpF homotrimer with 3 CEACAM1 bound
    • Protein or peptide: Cell surface protein
    • Protein or peptide: Carcinoembryonic antigen-related cell adhesion molecule 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
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 / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / negative regulation of hepatocyte proliferation / Regulation of MITF-M dependent genes involved in invasion / 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 / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / negative regulation of hepatocyte proliferation / Regulation of MITF-M dependent genes involved in invasion / 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 / transport vesicle membrane / bile acid and bile salt transport / 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 / regulation of cell migration / protein tyrosine kinase binding / basal plasma membrane / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / adherens junction / cell outer membrane / regulation of cell growth / kinase binding / cellular response to insulin stimulus / cell-cell junction / cell junction / cell migration / protein transport / actin binding / angiogenesis / protein phosphatase binding / calmodulin binding / cell adhesion / protein dimerization activity / apical plasma membrane / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / : / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Serralysin-like metalloprotease, C-terminal / Pilin-like / Immunoglobulin domain ...Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / : / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Serralysin-like metalloprotease, C-terminal / Pilin-like / 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 / Cell surface protein
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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_51347.png

Downloads & links

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Map

FileDownload / File: emd_51347.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map, sharpened with DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.023777101 - 1.9082515
Average (Standard dev.)0.0006916982 (±0.018144337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51347_msk_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map, not sharpened

Fileemd_51347_additional_1.map
AnnotationFull map, not sharpened
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Half map: #1

Fileemd_51347_half_map_1.map
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Half map: #2

Fileemd_51347_half_map_2.map
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Sample components

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Entire : Hetero-hexameric complex of CbpF homotrimer with 3 CEACAM1 bound

EntireName: Hetero-hexameric complex of CbpF homotrimer with 3 CEACAM1 bound
Components
  • Complex: Hetero-hexameric complex of CbpF homotrimer with 3 CEACAM1 bound
    • Protein or peptide: Cell surface protein
    • Protein or peptide: Carcinoembryonic antigen-related cell adhesion molecule 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Hetero-hexameric complex of CbpF homotrimer with 3 CEACAM1 bound

SupramoleculeName: Hetero-hexameric complex of CbpF homotrimer with 3 CEACAM1 bound
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Cell surface protein

MacromoleculeName: Cell surface protein / type: protein_or_peptide / ID: 1 / Details: full length protein, residues 25-274 are resolved / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 51.827051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKTAIAIAV ALAGFATVAQ ASAAPVIKAG TATDSTEAGV DNVANGVKSS AFGYDNKAIE KESSAFGTGN RATGEFSSAF GFHNIASKI HSSAFGSNNA ADGVNSSAFG FKNTVSGFNS SAFGSQYQVT GNFSGAFGMG EFNGQYQYKN EGNNSYMIGN K NKIASGSD ...String:
MKKTAIAIAV ALAGFATVAQ ASAAPVIKAG TATDSTEAGV DNVANGVKSS AFGYDNKAIE KESSAFGTGN RATGEFSSAF GFHNIASKI HSSAFGSNNA ADGVNSSAFG FKNTVSGFNS SAFGSQYQVT GNFSGAFGMG EFNGQYQYKN EGNNSYMIGN K NKIASGSD DNFILGNNVH IGGGINNSVA LGNNSTVSAS NTVSVGSSTL KRKIVNVGDG AISANSSDAV TGRQLYSGNG ID TAAWQNK LNVTRKNDYK DANDIDVNKW KAKLGVGSGG GGGAPVDAYT KSEADNKFAN KTDLNDYTKK DDYKDANGID VDK WKAKLG TGAGTADIEN LRNEVNEKID DVKDEVRTVG SLSAALAGLH PMQYDPKAPV QVMAALGHYR DKQSVAVGAS YYFN DRFMM STGIALSGEK RTKTMANVGF TLKLGKGSGV TYDETPQYVV QNEVKRLTVE NQELKERVRN LEEKLNMLLK NKRSS AWSH PQFEK

UniProtKB: Cell surface protein

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Macromolecule #2: Carcinoembryonic antigen-related cell adhesion molecule 1

MacromoleculeName: Carcinoembryonic antigen-related cell adhesion molecule 1
type: protein_or_peptide / ID: 2
Details: CEACAM1 extracellular domain with C-terminal histag (Acro Biosystems)
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.153664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLTTESMPFN VAEGKEVLLL VHNLPQQLFG YSWYKGERVD GNRQIVGYAI GTQQATPGPA NSGRETIYPN ASLLIQNVTQ NDTGFYTLQ VIKSDLVNEE ATGQFHVYPE LPKPSISSNN SNPVEDKDAV AFTCEPETQD TTYLWWINNQ SLPVSPRLQL S NGNRTLTL ...String:
QLTTESMPFN VAEGKEVLLL VHNLPQQLFG YSWYKGERVD GNRQIVGYAI GTQQATPGPA NSGRETIYPN ASLLIQNVTQ NDTGFYTLQ VIKSDLVNEE ATGQFHVYPE LPKPSISSNN SNPVEDKDAV AFTCEPETQD TTYLWWINNQ SLPVSPRLQL S NGNRTLTL LSVTRNDTGP YECEIQNPVS ANRSDPVTLN VTYGPDTPTI SPSDTYYRPG ANLSLSCYAA SNPPAQYSWL IN GTFQQST QELFIPNITV NNSGSYTCHA NNSVTGCNRT TVKTIIVTEL SPVVAKPQIK ASKTTVTGDK DSVNLTCSTN DTG ISIRWF FKNQSLPSSE RMKLSQGNTT LSINPVKRED AGTYWCEVFN PISKNQSDPI MLNVNYNALP QENGLSPGHH HHHH

UniProtKB: Cell adhesion molecule CEACAM1

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: The density map of CbpF without CEACAM1 (same publication) was used as initial model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 211927
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-9gh5:
Complex of Fusobacterium nucleatum CbpF with human CEACAM1

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