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- PDB-1gwb: STRUCTURE OF GLYCOPROTEIN 1B -

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Basic information

Entry
Database: PDB / ID: 1gwb
TitleSTRUCTURE OF GLYCOPROTEIN 1B
ComponentsPLATELET GLYCOPROTEIN IB ALPHA CHAIN
KeywordsBLOOD CLOTTING / TRANSMEMBRANE / GLYCOPROTEIN / HEMOSTASIS / BLOOD COAGULATION / LEUCINE-RICH REPEAT / CELL ADHESION / DISEASE MUTATION / POLYMORPHISM / VON WILLEBRAND DISEASE / BERNARD SOULIER SYNDROME
Function / homology
Function and homology information


thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / regulation of blood coagulation / Platelet Aggregation (Plug Formation) / release of sequestered calcium ion into cytosol / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / extracellular matrix / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell morphogenesis / platelet activation / blood coagulation / cell surface receptor signaling pathway / cell adhesion / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeats, bacterial type / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat ...Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeats, bacterial type / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / : / Platelet glycoprotein Ib alpha chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsEmsley, J. / Uff, S. / Clemetson, K.J.M. / Clemetson, J.M. / Harrison, T.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of the Platelet Glycoprotein Ib-Alpha N-Terminal Domain Reveals an Unmasking Mechanism of Receptor Activation
Authors: Uff, S. / Clemetson, J.M. / Harrison, T. / Clemetson, K.J. / Emsley, J.
History
DepositionMar 14, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 18, 2012Group: Other
Revision 1.3Jul 12, 2017Group: Advisory / Category: database_PDB_caveat / Item: _database_PDB_caveat.text
Revision 1.4Jul 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 / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
B: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,63011
Polymers63,0302
Non-polymers1,6009
Water2,576143
1
A: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4086
Polymers31,5151
Non-polymers8935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2225
Polymers31,5151
Non-polymers7074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)202.000, 202.000, 128.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein PLATELET GLYCOPROTEIN IB ALPHA CHAIN / GP-IB ALPHA / GPIBA / CD42B-ALPHA / CD42B


Mass: 31514.994 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 16-296 / Source method: isolated from a natural source
Details: TYR 292,294,295 MODIFIED TO TYROSINE-O-SULPHONIC ACID
Source: (natural) HOMO SAPIENS (human) / References: UniProt: P07359
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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

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Non-polymers , 4 types, 149 molecules

#2: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsGP-IB IS A SURFACE MEMBRANE PROTEIN OF PLATELETS,THAT TAKES PART IN THE FORMATION OF PLATELET PLUGS ...GP-IB IS A SURFACE MEMBRANE PROTEIN OF PLATELETS,THAT TAKES PART IN THE FORMATION OF PLATELET PLUGS BY BINDING TO THE A1 DOMAIN OF VON WILLEBRAND FACTOR.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16-10 mg/mlprotein1drop
20.1 MTris-HCl1reservoirpH6.5
32 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 37462 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.1
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 99.8 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 99.8 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.1

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 2.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.274 -5 %
Rwork0.245 --
obs0.245 37462 98.5 %
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4253 0 55 143 4451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0083
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_deg1.84
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor Rfree: 0.275
Solvent computation
*PLUS
Displacement parameters
*PLUS

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