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- PDB-2pv9: Crystal structure of murine thrombin in complex with the extracel... -

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Basic information

Entry
Database: PDB / ID: 2pv9
TitleCrystal structure of murine thrombin in complex with the extracellular fragment of murine PAR4
Components
  • Proteinase-activated receptor 4
  • 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 / Peptide ligand-binding receptors / thrombin-activated receptor activity / Thrombin signalling through proteinase activated receptors (PARs) / Regulation of Complement cascade ...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 / Peptide ligand-binding receptors / thrombin-activated receptor activity / Thrombin signalling through proteinase activated receptors (PARs) / Regulation of Complement cascade / G alpha (q) signalling events / Cell surface interactions at the vascular wall / cytolysis by host of symbiont cells / thrombospondin receptor activity / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / positive regulation of collagen biosynthetic process / positive regulation of blood coagulation / regulation of cytosolic calcium ion concentration / fibrinolysis / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / lipopolysaccharide binding / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / platelet aggregation / positive regulation of reactive oxygen species metabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / peptidase activity / regulation of cell shape / heparin binding / : / regulation of gene expression / positive regulation of cell growth / protease binding / endopeptidase activity / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / receptor ligand activity / external side of plasma membrane / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / plasma membrane
Similarity search - Function
Protease-activated receptor 4 / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Protease-activated receptor / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain ...Protease-activated receptor 4 / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Protease-activated receptor / 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 / Few Secondary Structures / Irregular / G-protein coupled receptors family 1 signature. / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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 4 / Prothrombin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 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 / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_sheet
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 / _struct_sheet.number_strands
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3425
Polymers37,8993
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-22 kcal/mol
Surface area15210 Å2
MethodPISA
2
C: Proteinase-activated receptor 4

A: Thrombin light chain
B: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3425
Polymers37,8993
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation5_555y,-x+y,z+1/61
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-12 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.153, 111.153, 179.707
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
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 / Mutation: S195A
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 4 / PAR-4 / Thrombin receptor-like 3 / Coagulation factor II receptor-like 3


Mass: 2841.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Midwest Biotech Inc. / References: UniProt: O88634
#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.: 2 / Source method: obtained synthetically / 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
Has protein modificationY

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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: 4.23 Å3/Da / Density % sol: 70.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 20% PEG 3350, 200 mM MgSO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 19, 2006
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. all: 8824 / Num. obs: 8568 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.2
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.3 / Num. unique all: 739 / % possible all: 86.3

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Processing

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

1shh


Resolution: 3.5→37.52 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 114304.42 / 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
Rfree0.319 472 5.5 %RANDOM
Rwork0.306 ---
obs0.306 8552 97.2 %-
all-8808 --
Displacement parametersBiso mean: 38.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.9 Å
Refinement stepCycle: LAST / Resolution: 3.5→37.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 28 0 2679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.17
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 69 5.5 %
Rwork0.356 1194 -
obs-1189 88.3 %

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