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

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Basic information

Entry
Database: PDB / ID: 1qyy
TitleCrystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 2.8 Angstrom Resolution
ComponentsPlatelet glycoprotein Ib alpha chain
KeywordsCELL ADHESION / Platelet Receptors / Glycocalicin / Leucine Rich Repeats
Function / homology
Function and homology information


thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / 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 ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / 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 / MAD / Resolution: 2.8 Å
AuthorsVarughese, K.I. / Ruggeri, Z.M. / Celikel, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Platinum-induced space-group transformation in crystals of the platelet glycoprotein Ib alpha N-terminal domain.
Authors: Varughese, K.I. / Ruggeri, Z.M. / Celikel, R.
History
DepositionSep 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_symm_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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
A: Platelet glycoprotein Ib alpha chain
G: Platelet glycoprotein Ib alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1697
Polymers64,6142
Non-polymers1,5555
Water1,00956
1
A: Platelet glycoprotein Ib alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4464
Polymers32,3071
Non-polymers1,1393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Platelet glycoprotein Ib alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7233
Polymers32,3071
Non-polymers4162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.610, 113.820, 56.210
Angle α, β, γ (deg.)90.00, 95.21, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChain A or Chain G represent the Biological unit.

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Components

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


Mass: 32306.787 Da / Num. of mol.: 2 / 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 alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-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
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_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)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
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
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 %(w/w)PEG60001reservoir
2120 mMsodium acetate1reservoir
3200 mMsodium nitrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.071564, 1.0079675
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 31, 2002
RadiationMonochromator: 2-Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0715641
21.00796751
ReflectionResolution: 2.7→50 Å / Num. all: 16932 / Num. obs: 16932 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.069 / Net I/σ(I): 8.7
Reflection shellResolution: 2.7→2.85 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 1163 / Rsym value: 0.317 / % possible all: 72.2
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. measured all: 118489 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 72.2 % / Num. unique obs: 1889 / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD
Starting model: Ab initio

Resolution: 2.8→15 Å / Cross valid method: R free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 741 5 %Random
Rwork0.219 ---
all0.223 15294 --
obs0.223 15294 --
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 67 56 4277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
Refinement
*PLUS
Rfactor Rfree: 0.2821 / Rfactor Rwork: 0.2201
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.377 / Rfactor Rwork: 0.318

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