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- PDB-2gi7: Crystal structure of human platelet Glycoprotein VI (GPVI) -

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Basic information

Entry
Database: PDB / ID: 2gi7
TitleCrystal structure of human platelet Glycoprotein VI (GPVI)
ComponentsGPVI protein
KeywordsBLOOD CLOTTING / CELL ADHESION / Ig-like domains
Function / homology
Function and homology information


collagen receptor activity / tetraspanin-enriched microdomain / collagen-activated tyrosine kinase receptor signaling pathway / collagen-activated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of platelet aggregation / enzyme-linked receptor protein signaling pathway / GPVI-mediated activation cascade / collagen binding / protein tyrosine kinase binding ...collagen receptor activity / tetraspanin-enriched microdomain / collagen-activated tyrosine kinase receptor signaling pathway / collagen-activated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of platelet aggregation / enzyme-linked receptor protein signaling pathway / GPVI-mediated activation cascade / collagen binding / protein tyrosine kinase binding / Cell surface interactions at the vascular wall / platelet activation / platelet aggregation / transmembrane signaling receptor activity / signaling receptor activity / membrane raft / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Platelet glycoprotein VI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHorii, K. / Kahn, M.L. / Herr, A.B.
CitationJournal: Blood / Year: 2006
Title: Structural basis for platelet collagen responses by the immune-type receptor glycoprotein VI.
Authors: Horii, K. / Kahn, M.L. / Herr, A.B.
History
DepositionMar 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AT 2MG/ML CONCENTRATION, THE PROTEIN IS MONOMERIC IN SOLUTION. HOWEVER, THE BIOLOGICAL UNIT IS LIKELY A DIMER ON THE SURFACE OF PLATELETS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GPVI protein
B: GPVI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8117
Polymers40,4002
Non-polymers4125
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.057, 45.286, 75.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21B-281-

HOH

31B-282-

HOH

41B-283-

HOH

DetailsThe biological assembly is a dimer in the asymmetric unit (Chain ID: A and B).

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Components

#1: Protein GPVI protein


Mass: 20199.836 Da / Num. of mol.: 2 / Fragment: Collagen binding domain, residues 21-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Human / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: GenBank: 70673338, UniProt: Q9HCN6*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / pH: 7.4
Details: 0.9M ammonium sulfate, 8% MPD, 20% glycerol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.40

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2005 / Details: OSMIC CONFOCAL MIRRORS
RadiationMonochromator: OSMIC CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 15739 / % possible obs: 99.3 % / Biso Wilson estimate: 48.1 Å2 / Rsym value: 0.079 / Net I/σ(I): 6.6
Reflection shellResolution: 2.4→2.52 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.348 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERV. 1.3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G0X

1g0x


Resolution: 2.4→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1902639.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: RESIDUES 0-1 IN MOLECULE A AND RESIDUES 99-107 AND 130-137 IN MOLECLUE B WERE DELETED DUE TO LOW ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.276 799 5.2 %RANDOM
Rwork0.223 ---
obs0.223 15500 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.02 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1-11.01 Å20 Å20 Å2
2--10.3 Å20 Å2
3----21.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 23 177 2919
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 123 5 %
Rwork0.312 2349 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HETERO.PARAMHETERO.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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