[English] 日本語
Yorodumi
- PDB-2mhq: Solution structure of the major factor VIII binding region on von... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mhq
TitleSolution structure of the major factor VIII binding region on von Willebrand factor
Componentsvon Willebrand factor
KeywordsBLOOD CLOTTING / von Willebrand factor / factor VIII / ensemble refinement
Function / homology
Function and homology information


Weibel-Palade body / Defective F8 binding to von Willebrand factor / 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 ...Weibel-Palade body / Defective F8 binding to von Willebrand factor / 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
von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsNot applicable, model1
AuthorsShiltagh, N. / Kirkpatrick, J. / Cabrita, L.D. / McKinnon, T.A.J. / Thalassinos, K. / Tuddenham, E.G.D. / Hansen, D.F.
CitationJournal: Blood / Year: 2014
Title: Solution structure of the major factor VIII binding region on von Willebrand factor.
Authors: Shiltagh, N. / Kirkpatrick, J. / Cabrita, L.D. / McKinnon, T.A. / Thalassinos, K. / Tuddenham, E.G. / Hansen, D.F.
History
DepositionDec 2, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: von Willebrand factor


Theoretical massNumber of molelcules
Total (without water)11,3511
Polymers11,3511
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1not applicable

-
Components

#1: Protein von Willebrand factor / / 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 detailsQ91R (UNP RESIDUE 852) IS NATURAL VARIANT ACCORDING TO DATABASE P04275 (VWF_HUMAN), UNIPROTKB/SWISS-PROT.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D 15N HSQC-NOESY-15N HSQC
1613D HN(CACO)NH
1713D (H)CC(CO)NH
1813D H(CCCO)NH
1913D (H)CCH-TOCSY
11022D constant-time 1H-13C HSQC
11113D 1H-15N NOESY
11243D 1H-13C NOESY
1133{1H}15N steady-state NOE
114315N R1rho relaxation
115315N R1 relaxation
116515N R2-CPMG relaxation dispersion
117515N R2-CPMG relaxation dispersion
11862D IPAP-15N HSQC
11972D IPAP-15N HSQC
12082D IPAP-15N HSQC
12162D IPAP-E.COSY-15N HSQC
12282D IPAP-E.COSY-15N HSQC
12363D IPAP-HNCO(J-CA)
12483D IPAP-HNCO(J-CA)
12563D HN(CO)CA(J-CB)
12683D HN(CO)CA(J-CB)
12763D IPAP-(HA)CA(CO)NH
12883D IPAP-(HA)CA(CO)NH
12912D 1H-15N HSQC
13012D 1H-13C HSQC
13112D constant-time 1H-13C HSQC
13242D 1H-13C HSQC
13342D constant-time 1H-13C HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
1300 mM [U-13C; U-15N] VWF TIL'E'-1, 20 mM sodium phosphate-2, 100 mM sodium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
2300 mM [U-10% 13C] VWF TIL'E'-4, 20 mM sodium phosphate-5, 100 mM sodium chloride-6, 90% H2O/10% D2O90% H2O/10% D2O
3300 mM [U-15N] VWF TIL'E'-7, 20 mM sodium phosphate-8, 100 mM sodium chloride-9, 90% H2O/10% D2O90% H2O/10% D2O
4300 mM [U-13C; U-15N] VWF TIL'E'-10, 20 mM sodium phosphate-11, 100 mM sodium chloride-12, 90% H2O/10% D2O90% H2O/10% D2O
5300 mM [U-15N] VWF TIL'E'-13, 20 mM sodium phosphate-14, 100 mM sodium chloride-15, 90% H2O/10% D2O90% H2O/10% D2O
6300 mM [U-13C; U-15N] VWF TIL'E'-16, 20 mM sodium phosphate-17, 100 mM sodium chloride-18, 90% H2O/10% D2O90% H2O/10% D2O
7300 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% D2O90% H2O/10% D2O
8300 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% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 mMVWF TIL'E'-1[U-13C; U-15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
300 mMVWF TIL'E'-4[U-10% 13C]2
20 mMsodium phosphate-52
100 mMsodium chloride-62
300 mMVWF TIL'E'-7[U-15N]3
20 mMsodium phosphate-83
100 mMsodium chloride-93
300 mMVWF TIL'E'-10[U-13C; U-15N]4
20 mMsodium phosphate-114
100 mMsodium chloride-124
300 mMVWF TIL'E'-13[U-15N]5
20 mMsodium phosphate-145
100 mMsodium chloride-155
300 mMVWF TIL'E'-16[U-13C; U-15N]6
20 mMsodium phosphate-176
100 mMsodium chloride-186
300 mMVWF TIL'E'-19[U-13C; U-15N]7
20 mMsodium phosphate-207
100 mMsodium chloride-217
5 mg/mLPf1 phage-227
300 mMVWF TIL'E'-23[U-13C; U-15N]8
20 mMsodium phosphate-248
100 mMsodium chloride-258
2 %pentaethylene glycol dodecyl ether-268
50 mMn-hexanol-278
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker Avance IIIBrukerAVANCE III5002
Bruker Avance IIIBrukerAVANCE III7003

-
Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.2DVariancollection
TopSpin2.1Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
Xplor-NIHrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Ensemble of 10 replicas was calculated collectively using ensemble-averaged approach (ensemble-refinement).
NMR representativeSelection criteria: not applicable
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10 / Representative conformer: 1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more