9GH5: Cell surface protein

Complex of Fusobacterium nucleatum CbpF with human CEACAM1. Determined by electron microscopy at 2.7 Å resolution. Released 2 Apr 2025.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Fusobacterium nucleatum, Homo sapiens
Chains: 6
Atoms: 10,383
Mol. weight: 291.92 kDa
Ligands: NAG
Released: 2 Apr 2025

Explore 9GH5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GH5 contains 27 α-helices and 143 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.

Chain A: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	1
β-strand	38-42	5	1
β-strand	45-46	2	1
β-strand	52-56	5	1
β-strand	59-60	2	1
β-strand	66-70	5	1
β-strand	73-74	2	1
β-strand	80-84	5	1
β-strand	87-88	2	1
β-strand	93-98	6	1
β-strand	101-102	2	1
β-strand	107-116	10	1
β-strand	122-130	9	1
β-strand	136-140	5	1
β-strand	143	1	2
β-strand	147	1	2
β-strand	150-151	2	1
β-strand	157-161	5	1
β-strand	164-165	2	1
β-strand	172-175	4	1
β-strand	180-181	2	1
β-strand	188-191	4	1
β-strand	202-204	3	1
β-strand	212	1	3
β-strand	213-215	3	4
β-strand	217	1	5
α-helix	218-219	2
α-helix	232-237	6
α-helix	246-249	4
α-helix	255-260	6
α-helix	269-272	4

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	6
β-strand	38-42	5	6
β-strand	45-46	2	6
β-strand	52-56	5	6
β-strand	59-60	2	6
β-strand	66-70	5	6
β-strand	73-74	2	6
β-strand	80-84	5	6
β-strand	87-88	2	6
β-strand	93-98	6	6
β-strand	101-102	2	6
β-strand	107-116	10	6
β-strand	122-130	9	6
β-strand	136-140	5	6
β-strand	143	1	7
β-strand	147	1	7
β-strand	150-151	2	6
β-strand	157-161	5	6
β-strand	164-165	2	6
β-strand	172-175	4	6
β-strand	180-181	2	6
β-strand	188-191	4	6
β-strand	202-204	3	6
β-strand	206	1	8
β-strand	211	1	8
β-strand	212	1	9
β-strand	213-215	3	1
β-strand	217	1	3
α-helix	218-219	2
α-helix	232-237	6
α-helix	246-249	4
α-helix	255-260	6
α-helix	266-272	7

Chain C: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	4
β-strand	38-42	5	4
β-strand	45-46	2	4
β-strand	52-56	5	4
β-strand	59-60	2	4
β-strand	66-70	5	4
β-strand	73-74	2	4
β-strand	80-84	5	4
β-strand	87-88	2	4
β-strand	93-98	6	4
β-strand	101-102	2	4
β-strand	107-116	10	4
β-strand	122-130	9	4
β-strand	136-140	5	4
β-strand	143	1	10
β-strand	147	1	10
β-strand	150-151	2	4
β-strand	157-161	5	4
β-strand	164-165	2	4
β-strand	172-175	4	4
β-strand	180-181	2	4
β-strand	188-191	4	4
β-strand	202-204	3	4
β-strand	206	1	11
β-strand	211	1	11
β-strand	212	1	5
β-strand	213-215	3	6
β-strand	217	1	9
α-helix	218-219	2
α-helix	232-237	6
α-helix	246-249	4
α-helix	255-258	4
α-helix	269-272	4

Chain D: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	37-41	5	12
β-strand	44-46	3	13
β-strand	51-56	6	12
β-strand	62-69	8	14
α-helix	75-77	3
β-strand	78-83	6	14
β-strand	88-91	4	14
β-strand	99-101	3	12
β-strand	107-109	3	12
α-helix	114-116	3
β-strand	118-126	9	14
β-strand	131-138	8	14
β-strand	139-141	3	13
β-strand	149-151	3	15
β-strand	164-167	4	15
β-strand	175-180	6	16
β-strand	183-184	2	16
α-helix	185-187	3
β-strand	191-194	4	15
β-strand	199-202	4	15
α-helix	207-209	3
β-strand	213	1	17
β-strand	214-218	5	16
β-strand	223	1	16
β-strand	229	1	17

Chains E and F: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	37-41	5	18
β-strand	44-46	3	19
β-strand	51-56	6	18
β-strand	62-69	8	20
α-helix	75-77	3
β-strand	78-83	6	20
β-strand	88-91	4	20
β-strand	99-101	3	18
β-strand	107-109	3	18
α-helix	114-116	3
β-strand	118-126	9	20
β-strand	131-138	8	20
β-strand	139-141	3	19
β-strand	149-151	3	21
β-strand	164-167	4	21
β-strand	175-180	6	22
β-strand	183-184	2	22
α-helix	185-187	3
β-strand	191-194	4	21
β-strand	199-202	4	21
α-helix	207-209	3
β-strand	213-218	6	22
β-strand	223-225	3	22
β-strand	229	1	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell surface protein	A, B, C	protein	489	Fusobacterium nucleatum	Q8RIS0 (AlphaFold model)
Carcinoembryonic antigen-related cell adhesion molecule 1	D, E, F	protein	400	Homo sapiens	P13688 (AlphaFold model)

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

>9GH5_1 Cell surface protein (chains A, B, C)
MKKTAIAIAVALAGFATVAQASAAPVIKAGTATDSTEAGVDNVANGVKSSAFGYDNKAIE
KESSAFGTGNRATGEFSSAFGFHNIASKIHSSAFGSNNAADGVNSSAFGFKNTVSGFNSS
AFGSQYQVTGNFSGAFGMGEFNGQYQYKNEGNNSYMIGNKNKIASGSDDNFILGNNVHIG
GGINNSVALGNNSTVSASNTVSVGSSTLKRKIVNVGDGAISANSSDAVTGRQLYSGNGID
TAAWQNKLNVTRKNDYKDANDIDVNKWKAKLGVGSGGGGGAPVDAYTKSEADNKFANKTD
LNDYTKKDDYKDANGIDVDKWKAKLGTGAGTADIENLRNEVNEKIDDVKDEVRTVGSLSA
ALAGLHPMQYDPKAPVQVMAALGHYRDKQSVAVGASYYFNDRFMMSTGIALSGEKRTKTM
ANVGFTLKLGKGSGVTYDETPQYVVQNEVKRLTVENQELKERVRNLEEKLNMLLKNKRSS
AWSHPQFEK

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

>9GH5_2 Carcinoembryonic antigen-related cell adhesion molecule 1 (chains D, E, F)
QLTTESMPFNVAEGKEVLLLVHNLPQQLFGYSWYKGERVDGNRQIVGYAIGTQQATPGPA
NSGRETIYPNASLLIQNVTQNDTGFYTLQVIKSDLVNEEATGQFHVYPELPKPSISSNNS
NPVEDKDAVAFTCEPETQDTTYLWWINNQSLPVSPRLQLSNGNRTLTLLSVTRNDTGPYE
CEIQNPVSANRSDPVTLNVTYGPDTPTISPSDTYYRPGANLSLSCYAASNPPAQYSWLIN
GTFQQSTQELFIPNITVNNSGSYTCHANNSVTGCNRTTVKTIIVTELSPVVAKPQIKASK
TTVTGDKDSVNLTCSTNDTGISIRWFFKNQSLPSSERMKLSQGNTTLSINPVKREDAGTY
WCEVFNPISKNQSDPIMLNVNYNALPQENGLSPGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	18

Primary citation

Structural basis for immune cell binding of Fusobacterium nucleatum via the trimeric autotransporter adhesin CbpF. Marongiu, G.L., Fink, U., Schopf, F. et al. Proc Natl Acad Sci U S A (2025) 122:e2418155122-e2418155122. DOI 10.1073/pnas.2418155122 · PubMed

Other PDB entries of the same protein (UniProt Q8RIS0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GH4 3.8 Å, Fusobacterium nucleatum adhesin CbpF

Browse structure collections

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