- PDB-6fwn: Structure and dynamics of the platelet integrin-binding C4 domain... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6fwn
Title
Structure and dynamics of the platelet integrin-binding C4 domain of von Willebrand factor
Components
von Willebrand factor
Keywords
BLOOD CLOTTING / von Willebrand Factor / vWC domain
Function / homology
Function and homology information
Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function
von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain ...von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily Similarity search - Domain/homology
Mass: 9122.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The first four residues in that sequence (GSMA) remain from the thrombin cleavage site and are not part of the native sequence. Source: (gene. exp.) Homo sapiens (human) / Cell line: Extracellular / Gene: VWF, F8VWF / Organ: Blood / Plasmid: pHAT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04275
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
3
isotropic
3
2D 1H-15N HSQC
1
2
3
isotropic
3
2D 1H-13C HSQC aliphatic
1
3
3
isotropic
3
2D 1H-13C HSQC aromatic
1
4
3
isotropic
3
2D 1H-13C HMQC
1
5
3
isotropic
3
3D HNCA
1
6
3
isotropic
3
3D HNCO
1
11
3
isotropic
3
3D HN(CA)CB
1
10
3
isotropic
3
3DCBCA(CO)NH
1
9
3
isotropic
3
3DHBHA(CO)NH
1
8
3
isotropic
3
3DH(CCO)NH
1
7
3
isotropic
3
3DC(CO)NH
1
12
3
isotropic
3
3D (H)CCH-TOCSY
1
15
3
isotropic
3
3D (H)CCH-TOCSY
1
14
3
isotropic
3
3D 1H-15N NOESY-HSQC
1
13
3
isotropic
3
3D 1H-13C NOESY-HSQC
1
16
4
isotropic
3
3D 1H-13C HMQC-NOESY
1
17
4
isotropic
3
3D 1H-13C HMQC-NOESY aromatic
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Sample preparation
Details
Type
Solution-ID
Contents
Label
Solvent system
solution
3
500 uM [U-13C; U-15N] von Willebrand Factor C4 domain, 20 mM sodium phosphate, 49.5 M H2O, 5.5 M D2O, 0.02 % w/v sodium azide, 90% H2O/10% D2O
15N13C_sample
90% H2O/10% D2O
solution
4
500 uM [U-13C; U-15N] von Willebrand Factor C4 domain, 20 mM sodium phosphate, 55 M D2O, 5 mM H2O, 0.02 % w/v sodium azide, 100% D2O
15N13C_D2O_sample
100% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
500uM
vonWillebrandFactorC4domain
[U-13C; U-15N]
3
20mM
sodiumphosphate
naturalabundance
3
49.5M
H2O
naturalabundance
3
5.5M
D2O
naturalabundance
3
0.02 % w/v
sodiumazide
naturalabundance
3
500uM
vonWillebrandFactorC4domain
[U-13C; U-15N]
4
20mM
sodiumphosphate
naturalabundance
4
55M
D2O
naturalabundance
4
5mM
H2O
naturalabundance
4
0.02 % w/v
sodiumazide
naturalabundance
4
Sample conditions
Ionic strength: 0.04 M / Label: conditions_1 / pH: 6.5 / Pressure: 1 bar / Temperature: 298 K
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NMR measurement
NMR spectrometer
Type: Bruker AvanceIII / Manufacturer: Bruker / Model: AvanceIII / Field strength: 600 MHz
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