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- PDB-1m10: Crystal structure of the complex of Glycoprotein Ib alpha and the... -

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Basic information

Entry
Database: PDB / ID: 1m10
TitleCrystal structure of the complex of Glycoprotein Ib alpha and the von Willebrand Factor A1 Domain
Components
  • Glycoprotein Ib alpha
  • von Willebrand Factor
KeywordsBLOOD CLOTTING / leucine-rich repeat / HEMOSTASIS / DINUCLEOTIDE BINDING FOLD
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 / 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 / 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 / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / hemostasis / Defective F9 activation / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / 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 / positive regulation of intracellular signal transduction / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Signaling by high-kinase activity BRAF mutants / 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 / blood coagulation / Signaling by BRAF and RAF1 fusions / integrin binding / 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 / 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) / 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 / Leucine-rich repeats, bacterial type / 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
von Willebrand factor / Platelet glycoprotein Ib alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHuizinga, E.G. / Tsuji, S. / Romijn, R.A.P. / Schiphorst, M.E. / de Groot, P.G. / Sixma, J.J. / Gros, P.
CitationJournal: Science / Year: 2002
Title: Structures of glycoprotein Ibalpha and its complex with von Willebrand factor A1 domain.
Authors: Huizinga, E.G. / Tsuji, S. / Romijn, R.A. / Schiphorst, M.E. / de Groot, P.G. / Sixma, J.J. / Gros, P.
History
DepositionJun 16, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 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: Glycoprotein Ib alpha


Theoretical massNumber of molelcules
Total (without water)56,0662
Polymers56,0662
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.84, 89.84, 124.63
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein von Willebrand Factor


Mass: 23731.447 Da / Num. of mol.: 1 / Fragment: A1 domain / Mutation: R543Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VWF / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P04275
#2: Protein Glycoprotein Ib alpha / Platelet glycoprotein Ib alpha chain


Mass: 32334.842 Da / Num. of mol.: 1 / Fragment: von Willebrand Factor binding domain / Mutation: N21Q N159Q M239V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GP1BA / Plasmid: pCDNA3.1 / Production host: Mesocricetus auratus (golden hamster) / Tissue (production host): kidney / References: UniProt: P07359
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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 3000, sodium chloride, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMTris1drop
2100 mM1droppH7.8NaCl
34 mg/mlprotein1drop
410 %(w/v)PEG30001reservoir
5200 mM1reservoirNaCl
6100 mMMES1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8075 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8075 Å / Relative weight: 1
ReflectionResolution: 3.09→30.5 Å / Num. all: 10454 / Num. obs: 10454 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 5.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 19.3
Reflection shellResolution: 3.09→3.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1037 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 40 Å
Reflection shell
*PLUS
Highest resolution: 3.1 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.48

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1AUQ and 1M0Z

1auq

1m0z


Resolution: 3.1→30.5 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1123736.97 / Data cutoff low absF: 0 / Isotropic thermal model: ISOTROPIC RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 529 5.1 %RANDOM
Rwork0.234 ---
all0.237 10391 --
obs0.237 10391 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.2789 Å2 / ksol: 0.300589 e/Å3
Displacement parametersBiso mean: 52.2 Å2
Baniso -1Baniso -2Baniso -3
1-10.1 Å217.03 Å20 Å2
2--10.1 Å20 Å2
3----20.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3.1→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 0 0 3688
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it1.512
X-RAY DIFFRACTIONc_scangle_it2.512.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 85 5 %
Rwork0.326 1622 -
obs-1707 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08

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