1U0N: Von Willebrand factor

The ternary von Willebrand Factor A1-glycoprotein Ibalpha-botrocetin complex. Determined by X-ray diffraction at 2.95 Å resolution. Released 19 Apr 2005.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Homo sapiens, Bothrops jararaca
Chains: 4
Atoms: 5,864
Mol. weight: 83.53 kDa
Released: 19 Apr 2005

Explore 1U0N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1U0N contains 22 α-helices and 48 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: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	509	1	1
β-strand	513-520	8	2
β-strand	522	1	3
α-helix	527-542	16
β-strand	544	1	1
β-strand	546	1	2
β-strand	551-552	2	2
β-strand	555-558	4	2
β-strand	562-566	5	2
α-helix	574-582	9
β-strand	589	1	3
α-helix	594-600	7
α-helix	601-605	5
β-strand	615-622	8	2
α-helix	631-633	3
α-helix	634-643	10
β-strand	646-653	8	2
α-helix	659-668	10
β-strand	675-677	3	2
α-helix	682-695	14
α-helix	699-701	3

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	1007-1008	2	4
β-strand	1013-1021	9	4
α-helix	1023-1033	11
β-strand	1038-1039	2	4
α-helix	1047-1057	11
β-strand	1066-1073	8	4
β-strand	1083	1	5
α-helix	1088	1
β-strand	1089	1	5
α-helix	1090	1
β-strand	1095	1	6
β-strand	1103-1107	5	4
α-helix	1109-1112	4
β-strand	1115-1118	4	4
β-strand	1124-1130	7	4

Chain C: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2009	1	7
β-strand	2012	1	7
β-strand	2015-2021	7	6
α-helix	2023-2033	11
β-strand	2037-2039	3	6
α-helix	2045-2054	10
β-strand	2064-2065	2	6
β-strand	2077-2079	3	4
β-strand	2097-2102	6	6
α-helix	2103-2105	3
β-strand	2107-2112	6	6
β-strand	2117-2123	7	6

Chain D: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	8
β-strand	12-16	5	8
α-helix	25-26	2
β-strand	35-37	3	8
β-strand	45-47	3	9
α-helix	48-51	4
β-strand	59-61	3	8
β-strand	69-71	3	9
β-strand	81-83	3	8
β-strand	104-106	3	8
β-strand	128-130	3	8
β-strand	152-154	3	8
β-strand	176-178	3	8
β-strand	199-201	3	8
α-helix	215-222	8
β-strand	227	1	8
β-strand	228-231	4	2
β-strand	237-241	5	2
α-helix	243-245	3
β-strand	247	1	10
β-strand	255	1	10
α-helix	256-258	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Von Willebrand factor	A	protein	208	Homo sapiens	P04275 (AlphaFold model)
Botrocetin	B	protein	133	Bothrops jararaca	P22029 (AlphaFold model)
Botrocetin	C	protein	125	Bothrops jararaca	P22030 (AlphaFold model)
Platelet glycoprotein Ib	D	protein	265	Homo sapiens	P07359 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1U0N_1 Von Willebrand factor (chains A)
DISEPPLHDFYCSRLLDLVFLLDGSSRLSEAEFEVLKAFVVDMMERLRISQKWVRVAVVE
YHDGSHAYIGLKDRKRPSELRRIASQVKYAGSQVASTSEVLKYTLFQIFSKIDRPEASRI
ALLLMASQEPQRMSRNFVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIEKQAPENKAFVL
SSVDELEQQRDEIVSYLCDLAPEAPPPT

Sequence of entity 2 (B), FASTA

>1U0N_2 Botrocetin (chains B)
DCPSGWSSYEGNCYKFFQQKMNWADAERFCSEQAKGGHLVSIKIYSKEKDFVGDLVTKNI
QSSDLYAWIGLRVENKEKQCSSEWSDGSSVSYENVVERTVKKCFALEKDLGFVLWINLYC
AQKNPFVCKSPPP

Sequence of entity 3 (C), FASTA

>1U0N_3 Botrocetin (chains C)
DCPPDWSSYEGHCYRFFKEWMHWDDAEEFCTEQQTGAHLVSFQSKEEADFVRSLTSEMLK
GDVVWIGLSDVWNKCRFEWTDGMEFDYDDYYLIAEYECVASKPTNNKWWIIPCTRFKNFV
CEFQA

Sequence of entity 4 (D), FASTA

>1U0N_4 Platelet glycoprotein Ib (chains D)
HPICEVSKVASHLEVNCDKRQLTALPPDLPKDTTILHLSENLLYTFSLATLMPYTRLTQL
NLDRCELTKLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGAL
RGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNQLTELPAGLLNGLENLDTLLLQ
ENSLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQDNAENVYVWKQGVDVKAMT
SNVASVQCDNSDKFPVYKYPGKGCP

Primary citation

The snake venom protein botrocetin acts as a biological brace to promote dysfunctional platelet aggregation. Fukuda, K., Doggett, T., Laurenzi, I.J. et al. Nat Struct Mol Biol (2005) 12:152-159. DOI 10.1038/nsmb892 · PubMed

Other PDB entries of the same protein (UniProt P04275 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5BV8 1.59 Å, G1324S mutation in von Willebrand Factor A1 domain
7EOW 1.6 Å, High-resolution structure of vWF A1 domain in complex with caplacizumab, the first…
3ZQK 1.7 Å, Von Willebrand Factor A2 domain with calcium
1ATZ 1.8 Å, Human von willebrand factor A3 domain
1IJB 1.8 Å, The von Willebrand Factor mutant (I546V) A1 domain
2ADF 1.9 Å, Crystal Structure and Paratope Determination of 82D6A3, an Antithrombotic Antibody…
3GXB 1.9 Å, Crystal structure of VWF A2 domain
3PPV 1.9 Å, Crystal structure of an engineered VWF A2 domain (N1493C and C1670S)
3PPW 1.9 Å, Crystal structure of the D1596A mutant of an engineered VWF A2 domain (N1493C and C1670S)
3PPX 1.91 Å, Crystal structure of the N1602A mutant of an engineered VWF A2 domain (N1493C and C1670S)
1FNS 2.0 Å, Crystal structure of the von willebrand factor (VWF) A1 domain I546V mutant in complex…
3PPY 2.0 Å, Crystal structure of the D1596A/N1602A double mutant of an engineered VWF A2 domain…

Browse structure collections

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