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- PDB-2pux: Crystal structure of murine thrombin in complex with the extracel... -

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Basic information

Entry
Database: PDB / ID: 2pux
TitleCrystal structure of murine thrombin in complex with the extracellular fragment of murine PAR3
Components
  • Proteinase-activated receptor 3
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE / SERINE PROTEASE
Function / homology
Function and homology information


Common Pathway of Fibrin Clot Formation / : / Platelet Aggregation (Plug Formation) / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Intrinsic Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / thrombin-activated receptor signaling pathway / thrombin-activated receptor activity / Peptide ligand-binding receptors ...Common Pathway of Fibrin Clot Formation / : / Platelet Aggregation (Plug Formation) / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Intrinsic Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / thrombin-activated receptor signaling pathway / thrombin-activated receptor activity / Peptide ligand-binding receptors / Thrombin signalling through proteinase activated receptors (PARs) / Regulation of Complement cascade / G alpha (q) signalling events / Cell surface interactions at the vascular wall / positive regulation of Rho protein signal transduction / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / thrombin / plasma membrane => GO:0005886 / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / fibrinolysis / regulation of cytosolic calcium ion concentration / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / G protein-coupled receptor activity / negative regulation of proteolysis / lipopolysaccharide binding / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of reactive oxygen species metabolic process / blood coagulation / peptidase activity / heparin binding / regulation of cell shape / positive regulation of cell growth / regulation of gene expression / collagen-containing extracellular matrix / endopeptidase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / apical plasma membrane / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / protein-containing complex / proteolysis / extracellular space
Similarity search - Function
Protease-activated receptor 3 / Protease-activated receptor / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle ...Protease-activated receptor 3 / Protease-activated receptor / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Proteinase-activated receptor 3 / Prothrombin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBah, A. / Chen, Z. / Bush-Pelc, L.A. / Mathews, F.S. / Di Cera, E.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4.
Authors: Bah, A. / Chen, Z. / Bush-Pelc, L.A. / Mathews, F.S. / Di Cera, E.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Molecular Dissection of Na+ Binding to Thrombin.
Authors: Pineda, A.O. / Carrell, C.J. / Bush, L.A. / Prasad, S. / Caccia, S. / Chen, Z. / Mathews, F.S. / Di Cera, E.
#2: Journal: J.Biol.Chem. / Year: 2007
Title: Structural Basis of Na+ Activation mimicry in murine.
Authors: Marino, F. / Chen, Z. / Ergenekan, C.E. / Bush, L.A. / Mathews, F.S. / Di Cera, E.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 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 1.5Aug 30, 2023Group: 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: Thrombin light chain
B: Thrombin heavy chain
C: Proteinase-activated receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8484
Polymers36,6273
Non-polymers2211
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.025, 48.188, 62.046
Angle α, β, γ (deg.)90.00, 106.23, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer.

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Components

#1: Protein/peptide Thrombin light chain


Mass: 5105.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: F2, Cf2 / Cell (production host): kidney cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P19221
#2: Protein Thrombin heavy chain


Mass: 29952.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: F2, Cf2 / Cell (production host): kidney cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P19221
#3: Protein/peptide Proteinase-activated receptor 3 / PAR-3 / THROMBIN RECEPTOR-LIKE 2 / COAGULATION FACTOR II RECEPTOR-LIKE 2


Mass: 1568.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MIDWEST Biotech Inc. / References: UniProt: O08675
#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


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


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 10000, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 28405 / Num. obs: 27610 / % possible obs: 97.2 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 3.5 % / Biso Wilson estimate: 5.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2506 / % possible all: 88.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPfrom ccp4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SHH

1shh


Resolution: 2→27.08 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 187825.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1238 4.8 %RANDOM
Rwork0.186 ---
obs0.186 25909 91.6 %-
all-28297 --
Displacement parametersBiso mean: 21.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 14 295 2872
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it2.391.5
X-RAY DIFFRACTIONc_mcangle_it3.262
X-RAY DIFFRACTIONc_scbond_it3.792
X-RAY DIFFRACTIONc_scangle_it5.282.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 176 4.6 %
Rwork0.256 3624 -
obs-3590 81.2 %

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