4C2B: Von willebrand factor

Crystal Structure of High-Affinity von Willebrand Factor A1 domain with Disulfide Mutation in Complex with High Affinity GPIb alpha. Determined by X-ray diffraction at 2.8 Å resolution. Released 8 Jan 2014.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: HOMO SAPIENS
Chains: 8
Atoms: 14,768
Mol. weight: 230.06 kDa
Released: 8 Jan 2014

Explore 4C2B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4C2B contains 60 α-helices and 115 β-strands across 8 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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	1274	1	1
β-strand	1276-1283	8	2
β-strand	1285	1	3
α-helix	1290-1305	16
β-strand	1309	1	2
β-strand	1314-1321	8	2
β-strand	1325-1327	3	2
α-helix	1337-1345	9
α-helix	1347-1349	3
β-strand	1352	1	3
α-helix	1357-1363	7
α-helix	1364-1368	5
β-strand	1378-1385	8	2
α-helix	1397-1406	10
β-strand	1410-1416	7	2
α-helix	1422-1431	10
β-strand	1438-1440	3	2
α-helix	1443-1445	3
α-helix	1446-1457	12
β-strand	1463	1	1

Chain B: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	4
β-strand	13-16	4	4
β-strand	33-37	5	4
β-strand	45-47	3	5
α-helix	48-51	4
β-strand	59-61	3	4
β-strand	69-71	3	5
β-strand	81-83	3	4
α-helix	92-94	3
β-strand	104-106	3	4
β-strand	128-130	3	4
β-strand	152-154	3	4
β-strand	176-178	3	4
β-strand	199-201	3	4
β-strand	207	1	6
α-helix	214-222	9
α-helix	224-226	3
β-strand	227	1	4
β-strand	228-233	6	2
β-strand	236-241	6	2
α-helix	243-245	3
β-strand	247	1	7
β-strand	248	1	6
β-strand	255	1	7
α-helix	256-258	3

Chain C: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	1276-1283	8	8
β-strand	1285	1	9
α-helix	1290-1306	17
β-strand	1309	1	8
β-strand	1314-1321	8	8
β-strand	1325-1327	3	8
α-helix	1337-1344	8
α-helix	1347-1349	3
β-strand	1352	1	9
α-helix	1359-1363	5
α-helix	1364-1368	5
β-strand	1378-1385	8	8
α-helix	1397-1406	10
β-strand	1409-1415	7	8
β-strand	1416	1	10
α-helix	1422-1429	8
β-strand	1440	1	10
α-helix	1443-1446	4
α-helix	1450-1457	8
α-helix	1458-1460	3
α-helix	1462-1465	4

Chain D: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	11
β-strand	12-16	5	11
β-strand	33-37	5	11
β-strand	45-47	3	12
α-helix	48-51	4
β-strand	59-61	3	11
β-strand	69-71	3	12
β-strand	81-83	3	11
β-strand	104-106	3	11
β-strand	128-130	3	11
β-strand	152-154	3	11
β-strand	176-178	3	11
β-strand	199-201	3	11
α-helix	214-222	9
α-helix	224-226	3
β-strand	227	1	11
β-strand	228-233	6	8
β-strand	236-241	6	8
α-helix	243-245	3
β-strand	247-248	2	13
β-strand	254-255	2	13
α-helix	256-258	3

Chain E: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1269-1271	3
β-strand	1274	1	14
β-strand	1276-1283	8	15
β-strand	1285	1	16
α-helix	1292-1305	14
β-strand	1309	1	15
β-strand	1314-1321	8	15
β-strand	1324-1327	4	15
α-helix	1337-1345	9
β-strand	1352	1	16
α-helix	1357-1363	7
α-helix	1364-1368	5
β-strand	1378-1385	8	15
α-helix	1397-1406	10
β-strand	1410-1416	7	15
α-helix	1422-1429	8
β-strand	1438-1440	3	15
α-helix	1443-1445	3
α-helix	1446-1459	14
β-strand	1463	1	14

Chain F: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	17
β-strand	13-16	4	17
β-strand	33-37	5	17
β-strand	45-47	3	18
α-helix	48-50	3
β-strand	59-61	3	17
β-strand	69-71	3	18
β-strand	81-83	3	17
β-strand	104-106	3	17
β-strand	128-130	3	17
β-strand	152-154	3	17
β-strand	176-178	3	17
β-strand	199-201	3	17
β-strand	207	1	19
α-helix	214-222	9
α-helix	224-226	3
β-strand	227	1	17
β-strand	228-233	6	15
β-strand	236-241	6	15
α-helix	243-245	3
β-strand	247	1	20
β-strand	248	1	19
β-strand	255	1	20
α-helix	256-258	3

Chain G: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	1274	1	21
β-strand	1276-1283	8	22
β-strand	1285	1	23
α-helix	1290-1305	16
β-strand	1309	1	22
β-strand	1314-1321	8	22
β-strand	1325-1327	3	22
α-helix	1337-1343	7
α-helix	1344-1346	3
β-strand	1352	1	23
α-helix	1357-1363	7
α-helix	1364-1368	5
β-strand	1378-1385	8	22
α-helix	1391-1393	3
α-helix	1397-1406	10
β-strand	1409-1416	8	22
α-helix	1422-1431	10
β-strand	1438-1440	3	22
α-helix	1450-1457	8
α-helix	1462	1
β-strand	1463	1	21

Chain H: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	24
β-strand	12-16	5	24
β-strand	35-37	3	24
β-strand	45-47	3	25
α-helix	48-51	4
β-strand	59-61	3	24
β-strand	69-71	3	25
β-strand	81-83	3	24
β-strand	104-106	3	24
β-strand	128-130	3	24
β-strand	152-154	3	24
β-strand	176-178	3	24
β-strand	199-201	3	24
α-helix	214-222	9
α-helix	224-226	3
β-strand	227	1	24
β-strand	228-233	6	22
β-strand	236-241	6	22
α-helix	243-245	3
β-strand	247	1	26
β-strand	255	1	26
α-helix	256-258	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Von willebrand factor	A, C, E, G	protein	215	HOMO SAPIENS	P04275 (AlphaFold model)
Platelet glycoprotein ib alpha chain	B, D, F, H	protein	291	HOMO SAPIENS	P07359 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>4C2B_1 VON WILLEBRAND FACTOR (chains A, C, E, G)
MEPPLHDFCRSRLLDLVFLLDGSSRLSEAEFEVLKAFVVDMMERLRISQKWVRVAVVEYH
DGSHAYIGLKDRKRPSELRRIASQVKYAGSQVASTSEVLKYTLFQIFSKIDRPEASRIAL
LLMASQEPQRMSRNFVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIEKQAPENKAFVLSS
VDELEQQRDEIVSYLCDLAPEAPPPTLPPHHHHHH

Sequence of entity 2 (B, D, F, H), FASTA

>4C2B_2 PLATELET GLYCOPROTEIN IB ALPHA CHAIN (chains B, D, F, H)
HPICEVSKVASHLEVNCDKRRLTALPPDLPKDTTILHLSENLLYTFSLATLMPYTRLTQL
NLDRCELTKLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGAL
RGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNRLTELPAGLLNGLENLDTLLLQ
ENSLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQDNAENVYVWKQVVDVKAVT
SNVASVQCDNSDKFPVYKYPGKGCPTLGDEGDTDLYDYYPEEDTEGDKVRG

Primary citation

Towards the Structural Basis of Regulation of Von Willebrand Factor Binding to Glycoprotein Ib. Blenner, M.A., Dong, X., Springer, T.A. J Biol Chem (2014) 289:5565. DOI 10.1074/JBC.M113.511220 · 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…

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