7DO4: CD97-CD55 complex

Crystal structure of CD97-CD55 complex. Determined by X-ray diffraction at 3.2 Å resolution. Released 22 Sept 2021.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,024
Mol. weight: 44.58 kDa
Ligands: NAG, CA
Released: 22 Sept 2021

Explore 7DO4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DO4 contains 15 α-helices and 45 β-strands across 2 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	1
β-strand	41-44	4	1
α-helix	45	1
β-strand	48-49	2	2
β-strand	55	1	1
β-strand	63-64	2	2
β-strand	80-85	6	3
β-strand	88-93	6	3
α-helix	94	1
β-strand	97-99	3	4
β-strand	106	1	3
α-helix	109-111	3
β-strand	114-116	3	4
β-strand	131-135	5	5
β-strand	140-144	5	5
α-helix	145	1
β-strand	150	1	6
α-helix	155	1
β-strand	163	1	6

Chain B: 10 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	7
β-strand	60-62	3	8
β-strand	63-64	2	7
β-strand	69-71	3	9
α-helix	72	1
β-strand	78-80	3	8
β-strand	81-82	2	10
β-strand	86-87	2	10
β-strand	94-96	3	9
α-helix	101-103	3
β-strand	107-109	3	11
α-helix	112-114	3
β-strand	124-126	3	12
β-strand	127-129	3	11
β-strand	133-135	3	13
β-strand	142-144	3	12
β-strand	145	1	14
β-strand	151	1	14
α-helix	152-154	3
β-strand	158-160	3	13
α-helix	161	1
β-strand	162	1	15
α-helix	163-165	3
β-strand	172-175	4	16
β-strand	181	1	15
β-strand	185-190	6	16
α-helix	191	1
β-strand	194-197	4	17
β-strand	201-203	3	16
β-strand	204-207	4	18
β-strand	210-213	4	18
β-strand	219-222	4	17
α-helix	228-231	4
β-strand	234-236	3	19
β-strand	248-249	2	20
β-strand	251-253	3	19
α-helix	254	1
β-strand	265-266	2	20
β-strand	267-270	4	21
β-strand	273-276	4	21
α-helix	279-281	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Adhesion G protein-coupled receptor E5	A	protein	145	Homo sapiens	P48960 (AlphaFold model)
Complement decay-accelerating factor	B	protein	251	Homo sapiens	P08174 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7DO4_1 Isoform 2 of Adhesion G protein-coupled receptor E5 (chains A)
QDSRGCARWCPQNSSCVNATACRCNPGFSSFSEIITTPTETCDDINECATPSKVSCGKFS
DCWNTEGSYDCVCSPGYEPVSGAKTFKNESENTCQDVDECSSGQHQCDSSTVCFNTVGSY
SCRCRPGWKPRHGIPNNQKDTVCED

Sequence of entity 2 (B), FASTA

>7DO4_2 Complement decay-accelerating factor (chains B)
SDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEEF
CNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWST
AVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQW
SDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDE
GEWSGPPPECR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CA	Calcium ion	Ca	2

Primary citation

Structural basis for CD97 recognition of the decay-accelerating factor CD55 suggests mechanosensitive activation of adhesion GPCRs. Niu, M., Xu, S., Yang, J. et al. J Biol Chem (2021) 296:100776-100776. DOI 10.1016/j.jbc.2021.100776 · PubMed

Other PDB entries of the same protein (UniProt P48960 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2BOU 1.9 Å, EGF Domains 1,2,5 of human EMR2, a 7-TM immune system molecule, in complex with barium.
8IKL 2.33 Å, Cryo-EM structure of the CD97-G13 complex
7YDM 2.89 Å, Cryo-EM structure of CD97/Gq complex
7YDJ 3.03 Å, Cryo EM structure of CD97/miniG12 complex
7YDH 3.1 Å, Cryo EM structure of CD97/miniG13 complex
7YDP 3.1 Å, Cryo-EM structure of CD97/miniGs complex
9MQR 3.16 Å, A8 Fab in complex with CD97
8IKJ 3.2 Å, Cryo-EM structure of the inactive CD97

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