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- PDB-4c29: Crystal Structure of High-Affinity von Willebrand Factor A1 domai... -

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Basic information

Entry
Database: PDB / ID: 4c29
TitleCrystal Structure of High-Affinity von Willebrand Factor A1 domain with Disulfide Mutation
ComponentsVON WILLEBRAND FACTOR
KeywordsBLOOD CLOTTING / CELL ADHESION
Function / homology
Function and homology information


Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / 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 / Weibel-Palade body / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / 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 / Weibel-Palade body / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / 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 / positive regulation of intracellular signal transduction / 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 / blood coagulation / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / protein-folding chaperone binding / 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 / Von Willebrand factor-like domain / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain ...von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / Von Willebrand factor-like domain / : / 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. / von Willebrand factor type C domain / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / von Willebrand factor, type A 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / von Willebrand factor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 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 1.2Jan 29, 2014Group: Data collection
Revision 1.3Mar 12, 2014Group: Database references
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VON WILLEBRAND FACTOR
B: VON WILLEBRAND FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,01710
Polymers49,4132
Non-polymers6048
Water3,153175
1
A: VON WILLEBRAND FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0185
Polymers24,7071
Non-polymers3114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VON WILLEBRAND FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9995
Polymers24,7071
Non-polymers2924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.249, 50.071, 96.869
Angle α, β, γ (deg.)90.00, 92.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VON WILLEBRAND FACTOR / VWF / VON WILLEBRAND ANTIGEN 2 / VON WILLEBRAND ANTIGEN II


Mass: 24706.678 Da / Num. of mol.: 2 / Fragment: RESIDUES 1264-1471 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: HIGH AFFINITY MUTANT OF A1 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04275
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.2 % / Description: NONE
Crystal growpH: 4.6
Details: CRYSTALS OF A1/SS APPEARED IN DROPS CONTAINING 25% PEG3350 AND 0.2 M CALCIUM ACETATE. THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING. CRYSTALS GROWN IN 8 MG/ML PROTEIN, 15% PEG3350, AND 0. ...Details: CRYSTALS OF A1/SS APPEARED IN DROPS CONTAINING 25% PEG3350 AND 0.2 M CALCIUM ACETATE. THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING. CRYSTALS GROWN IN 8 MG/ML PROTEIN, 15% PEG3350, AND 0.2 M CALCIUM ACETATE WERE HARVESTED, AND SOAKED IN THE SAME BUFFER CONTAINING 20% GLYCEROL FOR CRYOPROTECTION., pH 4.6

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID / Wavelength: 1.03322
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20133 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 29.76 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AUQ

1auq


Resolution: 2.202→41.202 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 1035 5.1 %
Rwork0.1855 --
obs0.1881 20133 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→41.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 35 175 3444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043332
X-RAY DIFFRACTIONf_angle_d0.6634473
X-RAY DIFFRACTIONf_dihedral_angle_d11.9881300
X-RAY DIFFRACTIONf_chiral_restr0.027500
X-RAY DIFFRACTIONf_plane_restr0.003569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2016-2.31770.30881440.23472652X-RAY DIFFRACTION97
2.3177-2.46290.29131510.23162655X-RAY DIFFRACTION99
2.4629-2.6530.29521490.23382728X-RAY DIFFRACTION100
2.653-2.91990.2761390.22252742X-RAY DIFFRACTION100
2.9199-3.34230.2861320.20932760X-RAY DIFFRACTION100
3.3423-4.21020.21941630.16052752X-RAY DIFFRACTION100
4.2102-41.20940.16281570.14322809X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.148 Å / Origin y: 6.7977 Å / Origin z: -23.7497 Å
111213212223313233
T0.2458 Å2-0.0088 Å2-0.0171 Å2-0.2377 Å20.0569 Å2--0.3284 Å2
L0.4703 °20.3074 °20.7015 °2-0.9557 °20.9516 °2--1.5198 °2
S0.0355 Å °-0.041 Å °-0.0512 Å °0.1215 Å °-0.018 Å °0.0135 Å °0.0787 Å °-0.0482 Å °-0.0132 Å °
Refinement TLS groupSelection details: ALL

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