9U93: Fusobacterium nucleatum CbpF

Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM5. Determined by electron microscopy at 2.4 Å resolution. Released 3 Sept 2025.

Method: Electron microscopy
Resolution: 2.4 Å
Organisms: Fusobacterium nucleatum, Homo sapiens
Chains: 6
Atoms: 8,376
Mol. weight: 156.84 kDa
Released: 3 Sept 2025

Explore 9U93 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9U93 contains 24 α-helices and 132 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B and C: 5 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	7
β-strand	37-41	5	7
β-strand	44-45	2	20
β-strand	51-55	5	7
β-strand	58-59	2	20
β-strand	65-69	5	7
β-strand	72-73	2	20
β-strand	79-83	5	7
β-strand	86-87	2	20
β-strand	93-97	5	7
β-strand	100-101	2	20
β-strand	107-111	5	7
β-strand	114-115	2	20
β-strand	121-125	5	7
β-strand	128-129	2	20
β-strand	135-139	5	7
β-strand	142-143	2	20
β-strand	149-153	5	7
β-strand	156	1	21
β-strand	160	1	21
β-strand	163-164	2	20
β-strand	170-174	5	7
β-strand	177-178	2	20
β-strand	185-190	6	7
β-strand	193-194	2	20
β-strand	201-204	4	7
β-strand	215-217	3	7
β-strand	225	1	15
β-strand	226-228	3	1
β-strand	230	1	4
α-helix	231-234	4
β-strand	241	1	5
β-strand	242	1	9
β-strand	244	1	16
α-helix	245-250	6
α-helix	256-262	7
α-helix	268-270	3
α-helix	279-285	7

Chains D, E and F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	37-41	5	17
β-strand	44-45	2	18
β-strand	51-56	6	17
α-helix	58-59	2
β-strand	62-69	8	19
α-helix	75-77	3
β-strand	78-83	6	19
β-strand	88-91	4	19
β-strand	99-102	4	17
β-strand	106-109	4	17
α-helix	114-116	3
β-strand	118-126	9	19
β-strand	131-138	8	19
β-strand	139-140	2	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fusobacterium nucleatum CbpF	A, B, C	protein	342	Fusobacterium nucleatum	A0A0M4S4Q9 (AlphaFold model)
Cell adhesion molecule CEACAM5	D, E, F	protein	148	Homo sapiens	P06731 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>9U93_1 Fusobacterium nucleatum CbpF (chains A, B, C)
MVSFSAPVFQAGTGTDSTVAGVNNEANGEKSSAFGYENKAKEKLSSAFGYKNIANGIEGS
AFGISNLAKGQYSSAFGFRNVANKRHSSAFGSGNEANGEQSSAFGFKNTVSGFNSSAFGS
QYEVTGNFSGAFGMGEFNGQYQYKNEGNNSYMIGNKNKIASGSNDNFILGNNVHIGGGIN
NSVALGNNSTVSASNTVSVGSSTLKRKIVNVGDGAISANSSDAVTGRQLYSGNGIDTAAW
QNKLNVTRKNDYKDANDIDVNKWKAKLGVGSGGGGGTADIENLRNEVNEKIDDVKDEVRE
NLYFQGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKHHHHHH

Sequence of entity 2 (D, E, F), FASTA

>9U93_2 Cell adhesion molecule CEACAM5 (chains D, E, F)
MKLTIESTPFNVAEGKEVLLLVHNLPQHLFGYSWYKGERVDGNRQIIGYVIGTQQATPGP
AYSGREIIYPNASLLIQNIIQNDTGFYTLHVIKSDLVNEEATGQFRVYPELENLYFQGSA
WSHPQFEKGGGSGGGSGGSAWSHPQFEK

Primary citation

Binding of Fusobacterium nucleatum autotransporter adhesin CbpF to human CEACAM1 and CEACAM5: A Velcro model for bacterium adhesion. Shen, F., Li, L., Yang, D. et al. Proc Natl Acad Sci U S A (2025) 122:e2516574122-e2516574122. DOI 10.1073/pnas.2516574122 · PubMed

Other PDB entries of the same protein (UniProt A0A0M4S4Q9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U94 2.11 Å, Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM1

Browse structure collections

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