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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 / bile acid transmembrane transporter activity / negative regulation of platelet aggregation / negative regulation of vascular permeability / regulation of immune system process / wound healing, spreading of cells / bile acid and bile salt transport / negative regulation of T cell receptor signaling pathway / microvillus membrane / transport vesicle membrane / homophilic cell adhesion via plasma membrane adhesion molecules / blood vessel development / 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 / integrin-mediated signaling pathway / adherens junction / Cell surface interactions at the vascular wall / negative regulation of protein kinase activity / regulation of cell growth / kinase binding / cellular response to insulin stimulus / cell migration / cell junction / cell-cell junction / actin binding / protein phosphatase binding / angiogenesis / protein dimerization activity / calmodulin binding / 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.USA / Year: 2025
Title: Structural basis for immune cell binding of Fusobacterium nucleatum via the trimeric autotransporter adhesin CbpF
Authors: Marongiu GL / Fink U / Schopf F / Oder A / von Kries JP / Roderer D
History
DepositionAug 15, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 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
Brightness
Contrast
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

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: 0.119
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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened map

Fileemd_51348_additional_1.map
AnnotationNon-sharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51348_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51348_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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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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