7NMU: Human platelet glycoprotein VI

Crystal structure of human platelet glycoprotein VI in complex with an inhibitory nanobody. Determined by X-ray diffraction at 2.5 Å resolution. Released 10 Mar 2021.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Lama glama
Chains: 4
Atoms: 4,934
Mol. weight: 71.12 kDa
Ligands: CA
Released: 10 Mar 2021

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

Secondary structure: helices and β-sheets

7NMU contains 18 α-helices and 65 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 AAA: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	13-17	5	1
β-strand	21-23	3	2
β-strand	28-33	6	1
β-strand	40-45	6	3
β-strand	50-52	3	3
β-strand	56-59	4	1
α-helix	64-66	3
β-strand	68-76	9	3
β-strand	79-80	2	3
α-helix	81-86	6
β-strand	87-89	3	3
β-strand	90-92	3	2
β-strand	99-103	5	4
β-strand	107-109	3	5
β-strand	114-119	6	4
β-strand	126-131	6	6
α-helix	132-135	4
β-strand	136-137	2	7
β-strand	148-151	4	8
α-helix	156-158	3
β-strand	160-167	8	7
β-strand	174	1	9
α-helix	176-179	4
β-strand	182-184	3	7
β-strand	185-187	3	10

Chain BBB: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	13-17	5	11
β-strand	21-23	3	9
β-strand	28-33	6	11
β-strand	40-45	6	12
β-strand	50-52	3	12
β-strand	56-59	4	11
α-helix	64-66	3
β-strand	68-76	9	12
β-strand	79-80	2	12
α-helix	81-86	6
β-strand	87-89	3	12
β-strand	90-92	3	9
β-strand	99-103	5	8
β-strand	107-109	3	10
β-strand	114-119	6	8
β-strand	126-131	6	7
α-helix	132-135	4
β-strand	136-137	2	6
β-strand	148-151	4	4
α-helix	156-158	3
β-strand	160-167	8	6
β-strand	174	1	2
β-strand	175	1	6
α-helix	176-179	4
β-strand	182-184	3	6
β-strand	185-187	3	5
α-helix	188-189	2

Chain CCC: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	10-12	3	16
β-strand	18-25	8	15
β-strand	33-39	7	16
β-strand	46-51	6	16
β-strand	59-60	2	16
α-helix	62-64	3
β-strand	68-73	6	15
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-99	8	16
β-strand	102-103	2	3
α-helix	110-112	3
β-strand	115-116	2	16
β-strand	120-124	5	16

Chain DDD: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	10-12	3	14
β-strand	18-25	8	13
β-strand	33-39	7	14
β-strand	46-51	6	14
β-strand	59-60	2	14
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-99	8	14
β-strand	102-103	2	12
α-helix	110-112	3
β-strand	115-116	2	14
β-strand	120-124	5	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Platelet glycoprotein VI	AAA, BBB	protein	194	Homo sapiens	Q9HCN6 (AlphaFold model)
Nanobody 2	CCC, DDD	protein	130	Lama glama

Sequence of entity 1 (AAA, BBB), FASTA

>7NMU_1 Platelet glycoprotein VI (chains AAA, BBB)
DKLASSGPLPKPSLQALPSSLVPLEKPVTLRCQGPPGVDLYRLEKLSSSRYQDQAVLFIP
AMKRSLAGRYRCSYQQGSLWSLPSDQLELVATGVFAKPSLSAQPGPAVSSGGDVTLQCQT
RYGFDQFALYKEGDPAPYKNPERWYRASFPIITVTAAHSGTYRCYSFSSRDPYLWSAPSD
PLELVVTGDPIEGR

Sequence of entity 2 (CCC, DDD), FASTA

>7NMU_2 Nanobody 2 (chains CCC, DDD)
QVQLQESGGGLVQPGGSLRLSCAAAGFTFDYYAIAWFRQAPGKEREGVSCISSSDGTTYY
ADSVKGRFTISKDNAKNTMYLQMNSLKPEDTAVYYCATSPLYSTNDRCISEDYDYWGQGT
QVTVSSLVPR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Structural characterization of a novel GPVI-nanobody complex reveals a biologically active domain-swapped GPVI dimer. Slater, A., Di, Y., Clark, J.C. et al. Blood (2021) 137:3443-3453. DOI 10.1182/blood.2020009440 · PubMed

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

5OU7 1.9 Å, Crystal structure of the Glycoprotein VI loop truncation mutant PAVS-PAPYKN
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

Browse structure collections

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