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- PDB-3zqk: Von Willebrand Factor A2 domain with calcium -

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Basic information

Entry
Database: PDB / ID: 3zqk
TitleVon Willebrand Factor A2 domain with calcium
ComponentsVON WILLEBRAND FACTOR
KeywordsBLOOD CLOTTING / ADAMTS-13 / FORCE SENSOR / VON WILLEBRAND DISEASE / VWA DOMAIN / HAEMOSTASIS
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 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
von Willebrand factor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJakobi, A.J. / Huizinga, E.G.
CitationJournal: Nat.Commun. / Year: 2011
Title: Calcium Modulates Force Sensing by the Von Willebrand Factor A2 Domain.
Authors: Jakobi, A.J. / Mashaghi, A. / Tans, S.J. / Huizinga, E.G.
History
DepositionJun 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Derived calculations
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,41514
Polymers65,7833
Non-polymers1,63211
Water9,152508
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A: VON WILLEBRAND FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5946
Polymers21,9281
Non-polymers6675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VON WILLEBRAND FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4104
Polymers21,9281
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: VON WILLEBRAND FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4104
Polymers21,9281
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.020, 35.540, 88.460
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 21927.689 Da / Num. of mol.: 3 / Fragment: A2 DOMAIN, RESIDUES 1478-1674
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293-EBNA1-S / Production host: HOMO SAPIENS (human) / References: UniProt: P04275
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.3 % / Description: NONE
Crystal growDetails: PROTEIN BUFFER: 0.015 M HEPES PH 7.5, 0.02 M NACL, 0.001 M CACL2. RESERVOIR BUFFER: 0.1 M MMT (PH 4.0-5.5), 0.15 M (NH4)2SO4, 18-23% (W/V) PEG2000 MME.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.7→30.8 Å / Num. obs: 51448 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 13.25 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.8 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GXB, PDB ENTRY 1ATZ

3gxb

1atz


Resolution: 1.7→29.306 Å / SU ML: 0.22 / σ(F): 1.92 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1996 2612 5.1 %
Rwork0.1549 --
obs0.1569 51446 95.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.677 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.7801 Å20 Å2-0.827 Å2
2---0.1568 Å20 Å2
3----1.6234 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4224 0 99 508 4831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124691
X-RAY DIFFRACTIONf_angle_d1.3966388
X-RAY DIFFRACTIONf_dihedral_angle_d18.0121799
X-RAY DIFFRACTIONf_chiral_restr0.097707
X-RAY DIFFRACTIONf_plane_restr0.007864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73090.27331310.21152485X-RAY DIFFRACTION95
1.7309-1.76420.26561330.20052471X-RAY DIFFRACTION92
1.7642-1.80020.26531210.18562518X-RAY DIFFRACTION95
1.8002-1.83930.22381280.16652506X-RAY DIFFRACTION94
1.8393-1.88210.21161300.15432517X-RAY DIFFRACTION93
1.8821-1.92920.19241460.15162538X-RAY DIFFRACTION96
1.9292-1.98130.1931300.14842496X-RAY DIFFRACTION93
1.9813-2.03960.18521270.14662564X-RAY DIFFRACTION96
2.0396-2.10540.22061380.14472543X-RAY DIFFRACTION94
2.1054-2.18070.19861310.13792558X-RAY DIFFRACTION96
2.1807-2.26790.2011410.14452550X-RAY DIFFRACTION95
2.2679-2.37110.18161290.14122603X-RAY DIFFRACTION95
2.3711-2.49610.20351460.14982565X-RAY DIFFRACTION97
2.4961-2.65240.20191370.14482590X-RAY DIFFRACTION97
2.6524-2.8570.19131350.14972617X-RAY DIFFRACTION97
2.857-3.14420.19651570.14452612X-RAY DIFFRACTION97
3.1442-3.59850.19081680.13982604X-RAY DIFFRACTION97
3.5985-4.5310.16261470.1272691X-RAY DIFFRACTION98
4.531-29.31070.17951370.16922806X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.21950.0306-0.00970.07860.02770.3467-0.01070.02450.03990.04190.02260.0525-0.0161-0.0423-0.0010.01360.00240.0054-0.003-0.00120.013323.94880.991231.6711
20.22780.1313-0.03470.1572-0.08660.36090.0294-0.0160.02440.03020.01930.0056-0.0853-0.0023-0.02030.02840.0035-0.00210.0028-0.00480.005725.5694-2.3821-2.3158
30.53720.0910.40350.23470.12490.5580.0408-0.00250.02020.17170.04350.00710.10690.15-0.0499-0.03190.0195-0.05080.0247-0.00780.0057-10.7792-13.386126.8696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1494:1674
2X-RAY DIFFRACTION2CHAIN B AND RESID 1494:1671
3X-RAY DIFFRACTION3CHAIN C AND RESID 1494:1671

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