- PDB-2mhp: Solution structure of the major factor VIII binding region on von... -
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Basic information
Entry
Database: PDB / ID: 2mhp
Title
Solution structure of the major factor VIII binding region on von Willebrand factor
Components
von Willebrand factor
Keywords
BLOOD CLOTTING / von Willebrand factor / factor VIII
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
vonWillebrandfactor / / vWF / von Willebrand antigen 2 / von Willebrand antigen II
Mass: 11351.278 Da / Num. of mol.: 1 / Fragment: domains TIL' and E', UNP residues 766-864 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VWF, F8VWF / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): Shuffle / References: UniProt: P04275
Sequence details
Q91R (UNP RESIDUE 852) IS NATURAL VARIANT ACCORDING TO DATABASE P04275 (VWF_HUMAN), UNIPROTKB/SWISS-PROT.
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D HNCO
1
2
1
3D HNCA
1
3
1
3DHN(CO)CA
1
4
1
3D HN(CA)CB
1
5
1
3D 15N HSQC-NOESY-15N HSQC
1
6
1
3DHN(CACO)NH
1
7
1
3D (H)CC(CO)NH
1
8
1
3DH(CCCO)NH
1
9
1
3D (H)CCH-TOCSY
1
10
2
2D constant-time 1H-13C HSQC
1
11
1
3D 1H-15N NOESY
1
12
4
3D 1H-13C NOESY
1
13
3
{1H}15N steady-state NOE
1
14
3
15NR1rhorelaxation
1
15
3
15NR1relaxation
1
16
5
15N R2-CPMG relaxation dispersion
1
17
5
15N R2-CPMG relaxation dispersion
1
18
6
2D IPAP-15N HSQC
1
19
7
2D IPAP-15N HSQC
1
20
8
2D IPAP-15N HSQC
1
21
6
2D IPAP-E.COSY-15N HSQC
1
22
8
2D IPAP-E.COSY-15N HSQC
1
23
6
3D IPAP-HNCO(J-CA)
1
24
8
3D IPAP-HNCO(J-CA)
1
25
6
3D HN(CO)CA(J-CB)
1
26
8
3D HN(CO)CA(J-CB)
1
27
6
3D IPAP-(HA)CA(CO)NH
1
28
8
3D IPAP-(HA)CA(CO)NH
1
29
1
2D 1H-15N HSQC
1
30
1
2D 1H-13C HSQC
1
31
1
2D constant-time 1H-13C HSQC
1
32
4
2D 1H-13C HSQC
1
33
4
2D constant-time 1H-13C HSQC
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
300 mM [U-13C; U-15N] VWF TIL'E'-1, 20 mM sodium phosphate-2, 100 mM sodium chloride-3, 90% H2O/10% D2O
90% H2O/10% D2O
2
300 mM [U-10% 13C] VWF TIL'E'-4, 20 mM sodium phosphate-5, 100 mM sodium chloride-6, 90% H2O/10% D2O
90% H2O/10% D2O
3
300 mM [U-15N] VWF TIL'E'-7, 20 mM sodium phosphate-8, 100 mM sodium chloride-9, 90% H2O/10% D2O
90% H2O/10% D2O
4
300 mM [U-13C; U-15N] VWF TIL'E'-10, 20 mM sodium phosphate-11, 100 mM sodium chloride-12, 90% H2O/10% D2O
90% H2O/10% D2O
5
300 mM [U-15N] VWF TIL'E'-13, 20 mM sodium phosphate-14, 100 mM sodium chloride-15, 90% H2O/10% D2O
90% H2O/10% D2O
6
300 mM [U-13C; U-15N] VWF TIL'E'-16, 20 mM sodium phosphate-17, 100 mM sodium chloride-18, 90% H2O/10% D2O
90% H2O/10% D2O
7
300 mM [U-13C; U-15N] VWF TIL'E'-19, 20 mM sodium phosphate-20, 100 mM sodium chloride-21, 5 mg/mL Pf1 phage-22, 90% H2O/10% D2O
90% H2O/10% D2O
8
300 mM [U-13C; U-15N] VWF TIL'E'-23, 20 mM sodium phosphate-24, 100 mM sodium chloride-25, 2 % w/v pentaethylene glycol dodecyl ether-26, 50 mM n-hexanol-27, 90% H2O/10% D2O
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
300mM
VWF TIL'E'-1
[U-13C; U-15N]
1
20mM
sodium phosphate-2
1
100mM
sodium chloride-3
1
300mM
VWF TIL'E'-4
[U-10% 13C]
2
20mM
sodium phosphate-5
2
100mM
sodium chloride-6
2
300mM
VWF TIL'E'-7
[U-15N]
3
20mM
sodium phosphate-8
3
100mM
sodium chloride-9
3
300mM
VWF TIL'E'-10
[U-13C; U-15N]
4
20mM
sodium phosphate-11
4
100mM
sodium chloride-12
4
300mM
VWF TIL'E'-13
[U-15N]
5
20mM
sodium phosphate-14
5
100mM
sodium chloride-15
5
300mM
VWF TIL'E'-16
[U-13C; U-15N]
6
20mM
sodium phosphate-17
6
100mM
sodium chloride-18
6
300mM
VWF TIL'E'-19
[U-13C; U-15N]
7
20mM
sodium phosphate-20
7
100mM
sodium chloride-21
7
5mg/mL
Pf1 phage-22
7
300mM
VWF TIL'E'-23
[U-13C; U-15N]
8
20mM
sodium phosphate-24
8
100mM
sodium chloride-25
8
2 %
pentaethylene glycol dodecyl ether-26
8
50mM
n-hexanol-27
8
Sample conditions
pH: 7.4 / Pressure: ambient / Temperature: 298 K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
600
1
Bruker Avance III
Bruker
AVANCEIII
500
2
Bruker Avance III
Bruker
AVANCEIII
700
3
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Processing
NMR software
Name
Version
Developer
Classification
VnmrJ
2.2D
Varian
collection
TopSpin
2.1
BrukerBiospin
collection
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
Sparky
Goddard
chemicalshiftassignment
Sparky
Goddard
peakpicking
Xplor-NIH
Schwieters, Kuszewski, TjandraandClore
structuresolution
Xplor-NIH
refinement
Refinement
Method: torsion angle dynamics / Software ordinal: 1 Details: Each structure in the ensemble was calculated individually.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1
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