5OU7: Platelet glycoprotein VI

Crystal structure of the Glycoprotein VI loop truncation mutant PAVS-PAPYKN. Determined by X-ray diffraction at 1.9 Å resolution. Released 5 Sept 2018.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,101
Mol. weight: 80.98 kDa
Ligands: PO4, NAG, PG6
Released: 5 Sept 2018

Explore 5OU7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OU7 contains 23 α-helices and 77 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: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5	1	1
α-helix	6-8	3
β-strand	9-13	5	2
β-strand	17-19	3	3
β-strand	24-29	6	2
β-strand	36-41	6	4
β-strand	46-48	3	4
β-strand	52-55	4	2
α-helix	60-62	3
β-strand	64-72	9	4
β-strand	75-76	2	4
β-strand	77	1	1
α-helix	78-82	5
β-strand	83-85	3	4
β-strand	86-91	6	3
β-strand	95-100	6	5
β-strand	106-111	6	5
β-strand	118-123	6	6
α-helix	128	1
β-strand	129-133	5	6
β-strand	137-140	4	5
α-helix	143-144	2
β-strand	146-154	9	6
β-strand	157-161	5	6
β-strand	162	1	3
α-helix	163-167	5
β-strand	168-171	4	6

Chain B: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5	1	7
α-helix	6-8	3
β-strand	9-13	5	8
β-strand	17-19	3	9
β-strand	24-29	6	8
β-strand	36-41	6	10
β-strand	46-48	3	10
β-strand	52-55	4	8
α-helix	60-62	3
β-strand	64-72	9	10
β-strand	75-76	2	10
β-strand	77	1	7
α-helix	78-82	5
β-strand	83-85	3	10
β-strand	86-88	3	9
β-strand	95-100	6	11
β-strand	106-111	6	11
β-strand	118-123	6	12
α-helix	128	1
β-strand	129-133	5	12
β-strand	137-140	4	11
α-helix	143-144	2
β-strand	146-153	8	12
β-strand	160	1	9
α-helix	162-167	6
β-strand	168-171	4	12

Chain C: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	5-6	2
β-strand	9-13	5	13
β-strand	17-19	3	14
β-strand	24-29	6	13
β-strand	36-41	6	15
β-strand	47-48	2	15
β-strand	52-55	4	13
α-helix	60-62	3
β-strand	64-72	9	15
β-strand	75-76	2	15
α-helix	77-82	6
β-strand	83-85	3	15
β-strand	86-91	6	14
β-strand	95-100	6	16
β-strand	105-111	7	16
β-strand	118-123	6	6
β-strand	129-133	5	6
β-strand	137-141	5	16
β-strand	146-153	8	6
β-strand	160-162	3	14
α-helix	163-167	5
β-strand	168-172	5	6

Chain D: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	5-6	2
β-strand	9-13	5	17
β-strand	17-19	3	18
β-strand	24-29	6	17
β-strand	36-41	6	19
β-strand	47-48	2	19
β-strand	52-55	4	17
α-helix	60-62	3
β-strand	64-72	9	19
β-strand	75-76	2	19
α-helix	77-82	6
β-strand	83-85	3	19
β-strand	86-88	3	18
α-helix	92-94	3
β-strand	95-100	6	20
β-strand	105-111	7	20
β-strand	118-123	6	12
β-strand	129-133	5	12
β-strand	137-141	5	20
β-strand	146-153	8	12
β-strand	160	1	18
α-helix	162-167	6
β-strand	168-172	5	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Platelet glycoprotein VI	A, B, C, D	protein	181	Homo sapiens	Q9HCN6 (AlphaFold model)

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

>5OU7_1 Platelet glycoprotein VI (chains A, B, C, D)
GSQSGPLPKPSLQALPSSLVPLEKPVTLRCQGPPGVDLYRLEKLSSSRYQDQAVLFIPAM
KRSLAGRYRCSYQNGSLWSLPSDQLELVATGVFAKPSLSAQPGSGGDVTLQCQTRYGFDQ
FALYKEGDPERWYRASFPIITVTAAHSGTYRCYSFSSRDPYLWSAPSDPLELVVTGTSAA
A

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
PG6	1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane	C12 H26 O6	2

Water and common crystallization additives (CL) are not listed.

Primary citation

Structural insights into collagen-binding by platelet receptor Glycoprotein VI. Feitsma, L.J., Brondijk, T.H.C., Jarvis, G. et al. To be published.

Other PDB entries of the same protein (UniProt Q9HCN6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7R58 1.9 Å, Crystal structure of the GPVI-glenzocimab complex
2GI7 2.4 Å, Crystal structure of human platelet Glycoprotein VI (GPVI)
5OU8 2.5 Å, Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)5
5OU9 2.5 Å, Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)3
7NMU 2.5 Å, Crystal structure of human platelet glycoprotein VI in complex with an inhibitory…

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