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- PDB-4c2b: Crystal Structure of High-Affinity von Willebrand Factor A1 domai... -

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Basic information

Entry
Database: PDB / ID: 4c2b
TitleCrystal Structure of High-Affinity von Willebrand Factor A1 domain with Disulfide Mutation in Complex with High Affinity GPIb alpha
Components
  • PLATELET GLYCOPROTEIN IB ALPHA CHAIN
  • VON WILLEBRAND FACTOR
KeywordsBLOOD CLOTTING
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
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: 2.8 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 / 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 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
C: VON WILLEBRAND FACTOR
D: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
E: VON WILLEBRAND FACTOR
F: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
G: VON WILLEBRAND FACTOR
H: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,05720
Polymers228,7958
Non-polymers1,26212
Water1,17165
1
A: VON WILLEBRAND FACTOR
B: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5865
Polymers57,1992
Non-polymers3873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-5 kcal/mol
Surface area26020 Å2
MethodPQS
2
C: VON WILLEBRAND FACTOR
D: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3914
Polymers57,1992
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-3.3 kcal/mol
Surface area25830 Å2
MethodPQS
3
E: VON WILLEBRAND FACTOR
F: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3914
Polymers57,1992
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-2.6 kcal/mol
Surface area25230 Å2
MethodPQS
4
G: VON WILLEBRAND FACTOR
H: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6897
Polymers57,1992
Non-polymers4905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-1.8 kcal/mol
Surface area25410 Å2
MethodPQS
Unit cell
Length a, b, c (Å)96.530, 103.840, 119.930
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

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


Mass: 24706.678 Da / Num. of mol.: 4 / Fragment: 1264-1468 / 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: Protein
PLATELET GLYCOPROTEIN IB ALPHA CHAIN / GP-IB ALPHA / GPIB-ALPHA / GPIBA / GLYCOPROTEIN IBALPHA / ANTIGEN CD42B-ALPHA


Mass: 32492.104 Da / Num. of mol.: 4 / 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 , 4 types, 77 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Description: THE RESOLUTION FOR A1 SS-GPIBALPHA-VWD2 WAS FOUND TO EXTEND TO 2.8 ANGSTROMS USING CROSS-CORRELATION.
Crystal growpH: 4.6
Details: CRYSTALS OF A1/SS-GPIB/VWD2 COMPLEX APPEARED IN DROPS WITH 20% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. THESE CRYSTALS WERE CRUSHED AND USED FOR ...Details: CRYSTALS OF A1/SS-GPIB/VWD2 COMPLEX APPEARED IN DROPS WITH 20% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING CRYSTAL GROWTH IN 8 MG/ML COMPLEX, 15% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08 M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. SINCE THESE CRYSTALS WERE FORMED IN BUFFER CONTAINING 20% GLYCEROL, NO ADDITIONAL CRYOPROTECTION WAS USED.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Apr 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.48
ReflectionResolution: 2.8→48.3 Å / Num. obs: 56526 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.59 / Net I/σ(I): 2.56
Reflection shellResolution: 2.8→2.87 Å / Mean I/σ(I) obs: 0.3 / % possible all: 80.9

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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 4C2A

4c2a


Resolution: 2.8→48.265 Å / SU ML: 0 / σ(F): 2 / Phase error: 27.94 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2859 1478 2.6 %
Rwork0.2527 --
obs0.2566 56511 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→48.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14634 0 69 65 14768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214997
X-RAY DIFFRACTIONf_angle_d0.46520361
X-RAY DIFFRACTIONf_dihedral_angle_d8.6715684
X-RAY DIFFRACTIONf_chiral_restr0.0312367
X-RAY DIFFRACTIONf_plane_restr0.0022581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-2.90040.30521280.27824827X-RAY DIFFRACTION83
2.9004-3.01640.27611360.26125509X-RAY DIFFRACTION95
3.0164-3.15350.2741640.25885560X-RAY DIFFRACTION95
3.1535-3.31960.31871350.24985590X-RAY DIFFRACTION96
3.3196-3.52730.32211460.2575526X-RAY DIFFRACTION95
3.5273-3.79910.27021500.27395518X-RAY DIFFRACTION95
3.7991-4.18060.30531360.27245525X-RAY DIFFRACTION94
4.1806-4.78340.28481360.23685566X-RAY DIFFRACTION95
4.7834-6.01870.26441580.2385655X-RAY DIFFRACTION96
6.0187-30.10430.27421500.24675741X-RAY DIFFRACTION96
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)
10.8424-0.06930.08730.9957-0.08940.7555-0.1086-0.0427-0.1066-0.3962-0.0755-0.32430.26970.19450.19261.680.0830.12090.50650.17490.5615111.9959-30.690626.2074
20.87020.4681-0.03450.60810.06440.35250.4441-0.1514-0.0652-0.2135-0.1897-0.217-0.10320.1036-0.19031.7457-0.34350.25360.5028-0.14170.629594.2365-10.480532.9491
32.3338-0.0231-0.86951.07320.27342.16540.0430.6154-0.2697-1.0714-0.1201-0.5586-0.1311-0.20720.04691.031-0.09490.19050.6025-0.04160.498177.93821.272933.6287
40.83470.529-0.08212.0792-0.29930.0428-0.26590.2703-0.1106-0.5820.1421-0.04730.09220.03460.13871.8433-0.2230.35620.47460.00980.746995.648141.354126.6342
50.2467-0.0357-0.01040.08660.06440.1927-0.04360.12940.0432-0.0694-0.02-0.0421-0.06450.0313-0.0091-0.0352-0.3090.04150.777-0.09750.917963.6481-21.727833.7598
61.40170.1322-0.2541.36250.28110.1136-0.00730.291-0.0656-0.54490.15740.0733-0.0527-0.0912-0.1170.2321-0.2885-0.0730.66090.16580.307545.9796-41.93427.0044
70.79290.3582-0.18271.925-1.29890.9242-0.12940.19880.0797-0.45310.42410.6212-0.158-0.1399-0.221.1994-0.1050.01650.34560.09050.475429.671730.069526.1393
81.2202-0.0795-0.16650.07980.29261.78690.33050.0806-0.1369-0.33470.0038-0.01660.18420.0123-0.12830.964-0.2445-0.04840.4775-0.02020.127547.327910.043933.2593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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