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9u93

Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM5

Method: ELECTRON MICROSCOPY D_max: 129.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u93
deposition_date	2025-03-27
title	Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM5
keywords	Fusobacterium nucleatum, trimeric autotransporter adhesin, CbpF, CEACAM5, CELL ADHESION; CELL ADHESION
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	36.39 Å
rg_electron	36.95 Å
i0	231401000.00
molecular_weight	118380.0 kDa
excluded_volume	146080 Å³
envelope_volume	188560 Å³
shell_volume	45395 Å³
envelope_diameter	133.5 Å
shell_rg	40.46 Å
envelope_rg	37.96 Å
shape_rg	36.92 Å
total_rg	37.24 Å
total_atoms	8370
n_residues	1113
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	129.3 Å
rg_real	36.65 Å
rg_real_error	1.35 Å
i0_real	2.3140e+08
i0_real_error	4.3370e+06
rg_reciprocal	36.49 Å
i0_reciprocal	231400000.0000
total_estimate	0.8380
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	39.1 Å
skewness	0.567
kurtosis	0.026
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	33790000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.748; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.821; Smooth: 0.824

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Fusobacterium nucleatum CbpF
formula_weight	35874.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,B,A
atom_count	8376

MVSFSAPVFQAGTGTDSTVAGVNNEANGEKSSAFGYENKAKEKLSSAFGYKNIANGIEGSAFGISNLAKGQYSSAFGFRNVANKRHSSAFGSGNEANGEQSSAFGFKNTVSGFNSSAFGSQYEVTGNFSGAFGMGEFNGQYQYKNEGNNSYMIGNKNKIASGSNDNFILGNNVHIGGGINNSVALGNNSTVSASNTVSVGSSTLKRKIVNVGDGAISANSSDAVTGRQLYSGNGIDTAAWQNKLNVTRKNDYKDANDIDVNKWKAKLGVGSGGGGGTADIENLRNEVNEKIDDVKDEVRENLYFQGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKHHHHHH

Source

organism	Fusobacterium nucleatum
ncbi_taxonomy_id	851
host_organism	Escherichia coli

Entity 2 polymer

description	Cell adhesion molecule CEACAM5
formula_weight	16404.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	F,D,E

MKLTIESTPFNVAEGKEVLLLVHNLPQHLFGYSWYKGERVDGNRQIIGYVIGTQQATPGPAYSGREIIYPNASLLIQNIIQNDTGFYTLHVIKSDLVNEEATGQFRVYPELENLYFQGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.40 Å
resolution_method	—
num_particles	240256

fit	/app/data/saxs_computation/u9/9u93/9u93.fit
pddf	/app/data/pr_computation/u9/9u93/9u93.pr.out
profile	/app/data/saxs_computation/u9/9u93/9u93.dat

Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM5

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)