[English] 日本語
Yorodumi
- PDB-4c2a: Crystal Structure of High-Affinity von Willebrand Factor A1 domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c2a
TitleCrystal Structure of High-Affinity von Willebrand Factor A1 domain with R1306Q and I1309V Mutations in Complex with High Affinity GPIb alpha
Components
  • PLATELET GLYCOPROTEIN IB ALPHA CHAIN
  • VON WILLEBRAND FACTOR
KeywordsBLOOD CLOTTING / CELL ADHESION / A1 / GPIBALPHA
Function / homology
Function and homology information


thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / 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 / positive regulation of leukocyte tethering or rolling ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / 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 / positive regulation of leukocyte tethering or rolling / hemostasis / blood coagulation, intrinsic pathway / Defective F9 activation / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / positive regulation of intracellular signal transduction / megakaryocyte development / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / regulation of blood coagulation / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / release of sequestered calcium ion into cytosol / fibrinolysis / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / cell morphogenesis / 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 surface receptor signaling pathway / cell adhesion / external side of plasma membrane / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
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. / Leucine rich repeat N-terminal domain / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / von Willebrand factor, type A domain / Leucine-rich repeats, bacterial type / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / von Willebrand factor type A domain / Alpha-Beta Horseshoe / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / von Willebrand factor, type A / Leucine-rich repeat profile. / von Willebrand factor A-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / DI(HYDROXYETHYL)ETHER / von Willebrand factor / Platelet glycoprotein Ib alpha chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.081 Å
AuthorsBlenner, M.A. / Dong, X. / Springer, T.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Towards the Structural Basis of Regulation of Von Willebrand Factor Binding to Glycoprotein Ib
Authors: Blenner, M.A. / Dong, X. / Springer, T.A.
History
DepositionAug 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Sep 30, 2015Group: Data collection / Source and taxonomy
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VON WILLEBRAND FACTOR
B: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5046
Polymers57,1622
Non-polymers3424
Water3,675204
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-0.6 kcal/mol
Surface area24880 Å2
MethodPQS
Unit cell
Length a, b, c (Å)89.060, 89.060, 124.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein VON WILLEBRAND FACTOR / VWF / VON WILLEBRAND ANTIGEN II / VON WILLEBRAND FACTOR A1


Mass: 24669.564 Da / Num. of mol.: 1 / Fragment: RESIDUES 1264-1471 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04275
#2: Protein PLATELET GLYCOPROTEIN IB ALPHA CHAIN / GP-IB ALPHA / GPIB-ALPHA / GPIBA / GLYCOPROTEIN IB ALPHA / ANTIGEN CD42B-ALPHA


Mass: 32492.104 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-306 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: HIGH AFFINITY MUTANT OF GPIB ALPHA WITH MUTATIONS TO REMOVE N-LINKED GLYCOSYLATION SITES, AND TWO PLATELET TYPE VWD MUTATIONS.
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: ET-6 / Cell line (production host): HEK-293T / Production host: HOMO SAPIENS (human) / References: UniProt: P07359

-
Non-polymers , 5 types, 208 molecules

#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.47 % / Description: NONE
Crystal growpH: 6.5
Details: CRYSTALS OF A1/VWD2-GPIBALPA/VWD2 COMPLEX APPEARED IN 12% PEG 8000, 0.1 M SODIUM CACODYLATE PH 6.5, 0.1 M CALCIUM ACETATE, AND 0.4 MG/ML RISTOCETIN (SIGMA-ALDRICH). THESE CRYSTALS WERE ...Details: CRYSTALS OF A1/VWD2-GPIBALPA/VWD2 COMPLEX APPEARED IN 12% PEG 8000, 0.1 M SODIUM CACODYLATE PH 6.5, 0.1 M CALCIUM ACETATE, AND 0.4 MG/ML RISTOCETIN (SIGMA-ALDRICH). THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING. CRYSTALS GREW IN 10 MG/ML COMPLEX, 14% PEG8000, 0.2 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, AND 0.4 MG/ML RISTOCETIN. NEXT WE SOAKED THESE CRYSTALS IN 14% PEG8000, 0.2 M CALCIUM ACETATE, 0.1 SODIUM CACODYLATE, PH 6.5, AND 4 MG/ML RISTOCETIN.

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 1.03322
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.08→48.4 Å / Num. obs: 66245 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 36.97 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.9
Reflection shellResolution: 2.08→2.19 Å / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.7 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SQ0

1sq0


Resolution: 2.081→48.446 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 19.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 3361 5.1 %
Rwork0.1605 --
obs0.162 66191 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.081→48.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 17 204 3929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033824
X-RAY DIFFRACTIONf_angle_d0.6885181
X-RAY DIFFRACTIONf_dihedral_angle_d10.9771450
X-RAY DIFFRACTIONf_chiral_restr0.026603
X-RAY DIFFRACTIONf_plane_restr0.003662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.081-2.11070.31081420.30332619X-RAY DIFFRACTION98
2.1107-2.14220.3481250.28332550X-RAY DIFFRACTION100
2.1422-2.17570.27851370.2782687X-RAY DIFFRACTION100
2.1757-2.21140.311310.26072569X-RAY DIFFRACTION100
2.2114-2.24950.28321410.23842666X-RAY DIFFRACTION100
2.2495-2.29040.22811480.21912603X-RAY DIFFRACTION100
2.2904-2.33450.25691230.22212674X-RAY DIFFRACTION100
2.3345-2.38210.23411470.20752565X-RAY DIFFRACTION100
2.3821-2.43390.20631360.19212639X-RAY DIFFRACTION100
2.4339-2.49050.18691580.17942589X-RAY DIFFRACTION100
2.4905-2.55280.21711500.1792638X-RAY DIFFRACTION100
2.5528-2.62180.20581390.17312630X-RAY DIFFRACTION100
2.6218-2.6990.21791310.17982630X-RAY DIFFRACTION100
2.699-2.78610.19461410.172629X-RAY DIFFRACTION100
2.7861-2.88570.18851380.17292591X-RAY DIFFRACTION100
2.8857-3.00120.17831570.16422630X-RAY DIFFRACTION100
3.0012-3.13770.21141470.17272602X-RAY DIFFRACTION100
3.1377-3.30310.18541260.17212646X-RAY DIFFRACTION100
3.3031-3.510.19371550.1592563X-RAY DIFFRACTION100
3.51-3.78090.16761380.14882638X-RAY DIFFRACTION100
3.7809-4.16120.17461430.13292613X-RAY DIFFRACTION100
4.1612-4.76290.12961360.11382623X-RAY DIFFRACTION100
4.7629-5.9990.17781300.12812647X-RAY DIFFRACTION100
5.999-48.45870.1541420.12322589X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -42.5925 Å / Origin y: 5.3747 Å / Origin z: -0.4352 Å
111213212223313233
T0.3787 Å20.0351 Å2-0.0589 Å2-0.1718 Å2-0.0002 Å2--0.2726 Å2
L1.5904 °20.1819 °20.2318 °2-1.2386 °20.2007 °2--1.2819 °2
S0.0844 Å °0.0357 Å °-0.0739 Å °0.1652 Å °0.0842 Å °-0.1213 Å °0.1324 Å °0.0101 Å °-0.161 Å °
Refinement TLS groupSelection details: ALL

+
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://pdbjlvh1.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