[English] 日本語
Yorodumi
- PDB-3hkj: Crystal structure of human thrombin mutant W215A/E217A in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hkj
TitleCrystal structure of human thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1
Components
  • Proteinase-activated receptor 1
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE / Serine protease / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Gamma-carboxyglutamic acid / Glycoprotein / Kringle / Protease / Secreted / Zymogen / Cell membrane / 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 / negative regulation of glomerular filtration / thrombin-activated receptor activity / platelet dense tubular network / cell-cell junction maintenance / establishment of synaptic specificity at neuromuscular junction / regulation of interleukin-1 beta production / platelet dense granule organization / connective tissue replacement involved in inflammatory response wound healing ...negative regulation of renin secretion into blood stream / dendritic cell homeostasis / negative regulation of glomerular filtration / thrombin-activated receptor activity / platelet dense tubular network / cell-cell junction maintenance / establishment of synaptic specificity at neuromuscular junction / regulation of interleukin-1 beta production / platelet dense granule organization / connective tissue replacement involved in inflammatory response wound healing / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / regulation of sensory perception of pain / positive regulation of smooth muscle contraction / positive regulation of calcium ion transport / : / positive regulation of Rho protein signal transduction / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of astrocyte differentiation / negative regulation of platelet activation / G-protein alpha-subunit binding / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / anatomical structure morphogenesis / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / positive regulation of vasoconstriction / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of GTPase activity / caveola / acute-phase response / Regulation of Complement cascade / positive regulation of interleukin-8 production / G protein-coupled receptor activity / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / regulation of synaptic plasticity / neuromuscular junction / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / activation of cysteine-type endopeptidase activity involved in apoptotic process / G-protein beta-subunit binding / positive regulation of interleukin-6 production / positive regulation of reactive oxygen species metabolic process / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / late endosome / phospholipase C-activating G protein-coupled receptor signaling pathway / heparin binding / regulation of cell shape / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / G alpha (q) signalling events / postsynaptic membrane / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / negative regulation of neuron apoptotic process / response to lipopolysaccharide / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / early endosome / blood microparticle / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding
Similarity search - Function
Thrombin receptor / Protease-activated receptor / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...Thrombin receptor / 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 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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
Prothrombin / Proteinase-activated receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGandhi, P.S. / Page, M.J. / Chen, Z. / Bush-Pelc, L. / Di Cera, E.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Mechanism of the Anticoagulant Activity of Thrombin Mutant W215A/E217A.
Authors: Gandhi, P.S. / Page, M.J. / Chen, Z. / Bush-Pelc, L. / Di Cera, E.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket.
Authors: Pineda, A.O. / Chen, Z.W. / Caccia, S. / Cantwell, A.M. / Savvides, S.N. / Waksman, G. / Mathews, F.S. / Di Cera, E.
History
DepositionMay 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 13, 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thrombin light chain
B: Thrombin heavy chain
C: Proteinase-activated receptor 1
D: Thrombin light chain
E: Thrombin heavy chain
F: Proteinase-activated receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2988
Polymers71,8566
Non-polymers4422
Water2,774154
1
A: Thrombin light chain
B: Thrombin heavy chain
C: Proteinase-activated receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1494
Polymers35,9283
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-7.5 kcal/mol
Surface area15040 Å2
MethodPISA
2
D: Thrombin light chain
E: Thrombin heavy chain
F: Proteinase-activated receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1494
Polymers35,9283
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-7.8 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.140, 61.783, 67.834
Angle α, β, γ (deg.)98.78, 110.28, 92.95
Int Tables number1
Space group name H-MP1
DetailsTHE BIOLOGICAL ASSEMBLY CONSISTS OF A, B AND C CHAINS.

-
Components

#1: Protein/peptide Thrombin light chain / Coagulation factor II


Mass: 3647.075 Da / Num. of mol.: 2 / Fragment: Light chain: UNP residues 333-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell (production host): BHK cells / Organ (production host): baby hamster kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin
#2: Protein Thrombin heavy chain / Coagulation factor II


Mass: 29607.055 Da / Num. of mol.: 2 / Fragment: Heavy chain: UNP residues 364-622 / Mutation: W215A, E217A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell (production host): BHK cells / Organ (production host): baby hamster kidney / 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: 2673.862 Da / Num. of mol.: 2 / Fragment: Extracellular fragment: UNP residues 42-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2R, CF2R, PAR1, TR / Cell (production host): BHK cells / Organ (production host): baby hamster kidney / 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.: 154 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES pH 7.5, 20% PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
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: Oct 27, 2008
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 24771 / Num. obs: 22864 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1956 / % possible all: 79.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TQ0

1tq0


Resolution: 2.6→37.17 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 127702.59 / 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
Rfree0.234 1079 4.9 %RANDOM
Rwork0.196 ---
obs0.196 22129 90.5 %-
Displacement parametersBiso mean: 40.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.6→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 28 154 4864
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 157 5.1 %
Rwork0.266 2898 -
obs-3039 75.1 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more