6GBH: Helicobacter pylori adhesin HopQ type II

Helicobacter pylori adhesin HopQ type II bound to the N-terminal domain of human CEACAM1. Determined by X-ray diffraction at 2.59 Å resolution. Released 27 Jun 2018.

Method: X-ray diffraction
Resolution: 2.59 Å
Organisms: Homo sapiens, Helicobacter pylori
Chains: 4
Atoms: 6,490
Mol. weight: 117.16 kDa
Released: 27 Jun 2018

Explore 6GBH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GBH contains 27 α-helices and 45 β-strands across 4 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: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	60-75	16
α-helix	82-101	20
α-helix	102-104	3
β-strand	105	1	11
β-strand	107	1	12
β-strand	110	1	13
β-strand	120-123	4	14
β-strand	132-135	4	14
α-helix	138-141	4
β-strand	143	1	13
β-strand	145	1	15
β-strand	149	1	15
β-strand	150	1	12
α-helix	152-171	20
β-strand	182-191	10	14
β-strand	208-217	10	14
α-helix	220-237	18
β-strand	241	1	11
α-helix	267-296	30
α-helix	321-349	29
α-helix	355-357	3
α-helix	370-372	3
α-helix	380-395	16
α-helix	398-411	14

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	17-22	6	1
β-strand	28-35	8	3
α-helix	41-43	3
β-strand	44-49	6	3
α-helix	50-52	3
β-strand	54-57	4	3
β-strand	65-67	3	1
β-strand	73-75	3	1
α-helix	80-82	3
β-strand	84-92	9	3
β-strand	97-104	8	3
β-strand	105-107	3	2

Chain C: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	60-76	17
α-helix	82-102	21
β-strand	105	1	7
β-strand	107	1	8
β-strand	110	1	9
β-strand	121-123	3	10
β-strand	132-134	3	10
α-helix	137-141	5
β-strand	143	1	9
β-strand	150	1	8
α-helix	152-171	20
α-helix	173-175	3
β-strand	182-191	10	10
β-strand	208-217	10	10
α-helix	220-237	18
β-strand	240-241	2	7
β-strand	265-266	2	7
α-helix	267-296	30
α-helix	318-348	31
α-helix	380-395	16
α-helix	398-409	12

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	10	1	5
β-strand	17-22	6	4
β-strand	28-35	8	6
α-helix	41-43	3
β-strand	44-49	6	6
β-strand	54-57	4	6
β-strand	65-67	3	4
β-strand	73-75	3	4
α-helix	80-82	3
β-strand	84-92	9	6
β-strand	97-104	8	6
β-strand	105	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Carcinoembryonic antigen-related cell adhesion molecule 1	B, D	protein	115	Homo sapiens	P13688 (AlphaFold model)
HopQ	A, C	protein	425	Helicobacter pylori	Q8GDI6 (AlphaFold model)

Sequence of entity 1 (B, D), FASTA

>6GBH_1 Carcinoembryonic antigen-related cell adhesion molecule 1 (chains B, D)
MQLTTESMPFNVAEGKEVLLLVHNLPQQLFGYSWYKGERVDGNRQIVGYAIGTQQATPGP
ANSGRETIYPNASLLIQNVTQNDTGFYTLQVIKSDLVNEEATGQFHVYPHHHHHH

Sequence of entity 2 (A, C), FASTA

>6GBH_2 HopQ (chains A, C)
MAVQKVKNADKVQKLSDAYENLNKLLANHSHSNPEAINANSATAINQAIGNLNANTQNLI
DKTDNSPAYQATLLALKSTVGLWNSIAYAVICGGYTDKPNHNTTETFYNQPGQGSDSITC
GGHVGLLQAGKNNSLSIEQFATLNKAYQIIQAALKQGLPALSDTKKTVEVTIKTATNANN
INVNNNNNNAADTTVSITDTFINDAQNLLTQAQTIINTLQDNCPQLKGKSSSNGGTNGAN
TPSWQTGANQNSCSVFGTEFSAISDMISNAQNIVQETQQLNTTPLKSIAQPNNFNLNSPN
SIALAQSMLKNAQSQAAVLKLANQVGSDFNRISTGVLKNYIEECNANASSESVSSNTWGK
GCAGVKQTLTSLENSNASFSSQTPQINQAQNLANTIVQELGHNPFKRVGIISSQTNNGAH
HHHHH

Primary citation

Helicobacter pyloriadhesin HopQ disruptstransdimerization in human CEACAMs. Moonens, K., Hamway, Y., Neddermann, M. et al. EMBO J (2018) 37. DOI 10.15252/embj.201798665 · PubMed

Other PDB entries of the same protein (UniProt P13688 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MU8 1.7 Å, Structure of the minimally glycosylated human CEACAM1 N-terminal domain
6XO1 1.76 Å, Crystal structure of N97A mutant of human CEACAM1
23VF 1.79 Å, Crystal structure of CEACAM1 in complex with MG1124 antibody
6XNO 1.9 Å, Crystal structure of E99A mutant of human CEACAM1
6XNW 1.9 Å, Crystal structure of V39A mutant of human CEACAM1
4QXW 2.04 Å, Crystal structure of the human CEACAM1 membrane distal amino terminal (N)-domain
9U94 2.11 Å, Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM1
2GK2 2.2 Å, Crystal structure of the N terminal domain of human CEACAM1
7RPP 2.2 Å, Crystal structure of human CEACAM1 with GFCC' and ABED face
4WHD 2.5 Å, Human CEACAM1 N-domain homodimer
6AW2 2.68 Å, Crystal structure of the HopQ-CEACAM1 complex
9GH5 2.7 Å, Complex of Fusobacterium nucleatum CbpF with human CEACAM1

Browse structure collections

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