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- PDB-4c2a: Crystal Structure of High-Affinity von Willebrand Factor A1 domai... -

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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 / 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 / blood coagulation, intrinsic pathway ...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 / 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 / blood coagulation, intrinsic pathway / hemostasis / platelet alpha granule / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / regulation of blood coagulation / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of intracellular signal transduction / immunoglobulin binding / Integrin cell surface interactions / fibrinolysis / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / release of sequestered calcium ion into cytosol / 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 / platelet activation / response to wounding / integrin binding / cell morphogenesis / blood coagulation / 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 / Platelet degranulation / protein-folding chaperone binding / : / 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 / 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 / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / von Willebrand factor type C domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Leucine rich repeat N-terminal domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / von Willebrand factor, type A domain / 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 / Leucine-rich repeats, bacterial type / Alpha-Beta Horseshoe / VWFA domain profile. / von Willebrand factor (vWF) type A domain / 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Details

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: 2.43 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.

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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

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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

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