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- PDB-3bef: Crystal structure of thrombin bound to the extracellular fragment... -

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Basic information

Entry
Database: PDB / ID: 3bef
TitleCrystal structure of thrombin bound to the extracellular fragment of PAR1
Components
  • (Prothrombin) x 2
  • Proteinase-activated receptor 1
KeywordsHYDROLASE / Serine protease / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Kringle / Secreted / Zymogen / G-protein coupled receptor / Membrane / Phosphoprotein / Receptor / Transducer / Transmembrane
Function / homology
Function and homology information


negative regulation of renin secretion into blood stream / dendritic cell homeostasis / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / platelet dense tubular network / establishment of synaptic specificity at neuromuscular junction / thrombin-activated receptor activity / regulation of interleukin-1 beta production / platelet dense granule organization / connective tissue replacement involved in inflammatory response wound healing / cell-cell junction maintenance ...negative regulation of renin secretion into blood stream / dendritic cell homeostasis / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / platelet dense tubular network / establishment of synaptic specificity at neuromuscular junction / thrombin-activated receptor activity / regulation of interleukin-1 beta production / platelet dense granule organization / connective tissue replacement involved in inflammatory response wound healing / cell-cell junction maintenance / positive regulation of smooth muscle contraction / positive regulation of calcium ion transport / cytolysis by host of symbiont cells / thrombospondin receptor activity / negative regulation of glomerular filtration / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / positive regulation of Rho protein signal transduction / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of vasoconstriction / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / anatomical structure morphogenesis / positive regulation of blood coagulation / negative regulation of fibrinolysis / G-protein alpha-subunit binding / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / regulation of cytosolic calcium ion concentration / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / release of sequestered calcium ion into cytosol / negative regulation of cytokine production involved in inflammatory response / homeostasis of number of cells within a tissue / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of interleukin-8 production / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / neuromuscular junction / lipopolysaccharide binding / G protein-coupled receptor activity / positive regulation of insulin secretion / regulation of synaptic plasticity / caveola / platelet activation / positive regulation of interleukin-6 production / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome / G-protein beta-subunit binding / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / : / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / response to lipopolysaccharide / phospholipase C-activating G protein-coupled receptor signaling pathway / blood microparticle / G alpha (q) signalling events / negative regulation of neuron apoptotic process / postsynaptic membrane / early endosome / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / inflammatory response / signaling receptor binding / negative regulation of cell population proliferation / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / positive regulation of DNA-templated transcription
Similarity search - Function
Thrombin receptor / 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 ...Thrombin receptor / 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
Prothrombin / Proteinase-activated receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGandhi, P.S. / Bah, A. / Chen, Z. / Mathews, F.S. / Di Cera, E.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural identification of the pathway of long-range communication in an allosteric enzyme.
Authors: Gandhi, P.S. / Chen, Z. / 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: 2006
Title: Crystal Structure of Thrombin in a Self-inhibited Conformation
Authors: Pineda, A.O. / Chen, Z. / Mathews, F.S. / Di Cera, E.
History
DepositionNov 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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: Prothrombin
B: Prothrombin
C: Proteinase-activated receptor 1
D: Prothrombin
E: Prothrombin
F: Proteinase-activated receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1938
Polymers72,7516
Non-polymers4422
Water4,125229
1
A: Prothrombin
B: Prothrombin
C: Proteinase-activated receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5974
Polymers36,3753
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Prothrombin
E: Prothrombin
F: Proteinase-activated receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5974
Polymers36,3753
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.060, 50.342, 85.078
Angle α, β, γ (deg.)76.89, 84.30, 73.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide Prothrombin / COAGULATION FACTOR II


Mass: 5367.890 Da / Num. of mol.: 2 / Fragment: THROMBIN LIGHT CHAIN / Mutation: D102N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin
#2: Protein Prothrombin / COAGULATION FACTOR II


Mass: 29779.234 Da / Num. of mol.: 2 / Fragment: THROMBIN HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin
#3: Protein/peptide Proteinase-activated receptor 1 / PAR-1 / Thrombin receptor / Coagulation factor II receptor


Mass: 1228.286 Da / Num. of mol.: 2 / Fragment: UNP residues 49-57
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2R, CF2R, PAR1, TR / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P25116
#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: 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.: 229 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES, 30% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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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: Dec 3, 2006
RadiationMonochromator: APS 14_BM_C / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 36229 / Num. obs: 34055 / % possible obs: 94 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 2.4 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3155 / % possible all: 87.7

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Processing

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

1shh


Resolution: 2.2→28 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 284604.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1657 5 %RANDOM
Rwork0.207 ---
obs0.207 33277 91.8 %-
all-36220 --
Displacement parametersBiso mean: 37.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4929 0 28 229 5186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 273 5.4 %
Rwork0.276 4800 -
obs-5014 84.5 %

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