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- PDB-1p9a: Crystal Structure of N-Terminal Domain of Human Platelet Receptor... -

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Basic information

Entry
Database: PDB / ID: 1p9a
TitleCrystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 1.7 Angstrom Resolution
ComponentsPlatelet glycoprotein Ib alpha chain precursor
KeywordsBLOOD CLOTTING / Platelet Receptors / Glycocalicin / Leucine Rich Repeats
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
Platelet glycoprotein Ib alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVarughese, K.I. / Celikel, R. / Ruggeri, Z.M.
CitationJournal: Science / Year: 2003
Title: Modulation of alpha-thrombin function by distinct interactions with platelet glycoprotein Ibalpha
Authors: Celikel, R. / McClintock, R.A. / Roberts, J.R. / Mendolicchio, G.L. / Ware, J. / Varughese, K.I. / Ruggeri, Z.M.
History
DepositionMay 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Platelet glycoprotein Ib alpha chain precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0552
Polymers32,3071
Non-polymers7491
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.734, 51.734, 114.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Platelet glycoprotein Ib alpha chain precursor / Glycoprotein Ibalpha / GP-Ib alpha / GPIbA / GPIb-alpha / CD42B-alpha / CD42B / Contains: Glycocalicin


Mass: 32306.787 Da / Num. of mol.: 1 / Fragment: N-Terminal Domain / Mutation: C65A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GP1BA / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P07359
#2: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 6000, Sodium Nitrate, Sodium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 mMHEPES1drop
250 mM1droppH7.4NaCl
315-20 mg/mlprotein1drop
412 %(w/w)PEG60001reservoir
5200 mMsodium nitrate1reservoir
6100 mMsodium acetate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.0642 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2002
RadiationMonochromator: Curved Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0642 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 31316 / Num. obs: 160737 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rsym value: 0.061 / Net I/σ(I): 19.8
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.317 / % possible all: 73.6

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2.7 Angstrom P21/GPIb-alpha MAD structure-to be published

Resolution: 1.7→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1521 -RANDOM
Rwork0.204 ---
all0.205 30630 --
obs0.205 31316 93.5 %-
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 50 207 2334
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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