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- PDB-3vw7: Crystal structure of human protease-activated receptor 1 (PAR1) b... -

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Basic information

Entry
Database: PDB / ID: 3vw7
TitleCrystal structure of human protease-activated receptor 1 (PAR1) bound with antagonist vorapaxar at 2.2 angstrom
ComponentsProteinase-activated receptor 1, Lysozyme
KeywordsSignaling protein/antagonist / High resolution structure / protease-activated receptor 1 / inactive conformation / antagonist vorapaxar / G protein-coupled receptor / signaling protein / membrane protein / thrombin receptor-antagonist complex / Signaling protein-antagonist complex
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 / establishment of synaptic specificity at neuromuscular junction / platelet dense tubular network / cell-cell junction maintenance / regulation of interleukin-1 beta production / connective tissue replacement involved in inflammatory response wound healing / platelet dense granule organization ...negative regulation of renin secretion into blood stream / dendritic cell homeostasis / negative regulation of glomerular filtration / thrombin-activated receptor activity / establishment of synaptic specificity at neuromuscular junction / platelet dense tubular network / cell-cell junction maintenance / regulation of interleukin-1 beta production / connective tissue replacement involved in inflammatory response wound healing / platelet dense granule organization / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / regulation of sensory perception of pain / positive regulation of smooth muscle contraction / protein kinase C-activating G protein-coupled receptor signaling pathway / positive regulation of calcium ion transport / positive regulation of Rho protein signal transduction / regulation of blood coagulation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / G-protein alpha-subunit binding / anatomical structure morphogenesis / positive regulation of collagen biosynthetic process / positive regulation of blood coagulation / Common Pathway of Fibrin Clot Formation / homeostasis of number of cells within a tissue / release of sequestered calcium ion into cytosol / positive regulation of vasoconstriction / viral release from host cell by cytolysis / Peptide ligand-binding receptors / peptidoglycan catabolic process / positive regulation of release of sequestered calcium ion into cytosol / caveola / G protein-coupled receptor activity / positive regulation of interleukin-8 production / positive regulation of receptor signaling pathway via JAK-STAT / neuromuscular junction / platelet activation / positive regulation of GTPase activity / response to wounding / positive regulation of interleukin-6 production / G-protein beta-subunit binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / cell wall macromolecule catabolic process / Thrombin signalling through proteinase activated receptors (PARs) / late endosome / lysozyme / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / postsynaptic membrane / G alpha (q) signalling events / positive regulation of canonical NF-kappaB signal transduction / negative regulation of neuron apoptotic process / host cell cytoplasm / response to lipopolysaccharide / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / positive regulation of cell migration / defense response to bacterium / inflammatory response / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / extracellular region / plasma membrane
Similarity search - Function
Thrombin receptor / Protease-activated receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme ...Thrombin receptor / Protease-activated receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / 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) / Lysozyme-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / ethyl / Endolysin / Proteinase-activated receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, C. / Srinivasan, Y. / Arlow, D.H. / Fung, J.J. / Palmer, D. / Zheng, Y. / Green, H.F. / Pandey, A. / Dror, R.O. / Shaw, D.E. ...Zhang, C. / Srinivasan, Y. / Arlow, D.H. / Fung, J.J. / Palmer, D. / Zheng, Y. / Green, H.F. / Pandey, A. / Dror, R.O. / Shaw, D.E. / Weis, W.I. / Coughlin, S.R. / Kobilka, B.K.
CitationJournal: Nature / Year: 2012
Title: High-resolution crystal structure of human protease-activated receptor 1
Authors: Zhang, C. / Srinivasan, Y. / Arlow, D.H. / Fung, J.J. / Palmer, D. / Zheng, Y. / Green, H.F. / Pandey, A. / Dror, R.O. / Shaw, D.E. / Weis, W.I. / Coughlin, S.R. / Kobilka, B.K.
History
DepositionAug 7, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Aug 16, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteinase-activated receptor 1, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,09913
Polymers54,3391
Non-polymers3,76012
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.044, 71.460, 172.187
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Proteinase-activated receptor 1, Lysozyme / PAR-1 / Coagulation factor II receptor / Thrombin receptor / Endolysin / Lysis protein / Muramidase


Mass: 54338.980 Da / Num. of mol.: 1 / Mutation: N250G, N259S, D1020N, C1054T, C1097A
Source method: isolated from a genetically manipulated source
Details: Chimera protein of residues 86-395 form Proteinase-activated receptor 1 (P25116, PAR1_HUMAN), Lyzosyme from Enterobacteria phage T4 (P00720, LYS_BPT4) and residues 303-395 from Proteinase- ...Details: Chimera protein of residues 86-395 form Proteinase-activated receptor 1 (P25116, PAR1_HUMAN), Lyzosyme from Enterobacteria phage T4 (P00720, LYS_BPT4) and residues 303-395 from Proteinase-activated receptor 1 (P25116, PAR1_HUMAN)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25116, UniProt: P00720, lysozyme

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Non-polymers , 5 types, 103 molecules

#2: Chemical ChemComp-VPX / ethyl [(1R,3aR,4aR,6R,8aR,9S,9aS)-9-{(E)-2-[5-(3-fluorophenyl)pyridin-2-yl]ethenyl}-1-methyl-3-oxododecahydronaphtho[2,3-c]fur an-6-yl]carbamate / vorapaxar / Vorapaxar


Mass: 492.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H33FN2O4 / Comment: antagonist*YM
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 18

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K
Details: 0.1-0.2M sodium chloride, 100mM sodium phosphate pH 6.0-6.5, 25%-35% PEG 300, Lipidic cubic phase (in meso phase), temperature 293K
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 28455 / Num. obs: 27181 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.135 / Χ2: 1.284 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.253.30.57515850.935185.7
2.25-2.313.60.53717170.968191.7
2.31-2.374.30.50417550.997194.9
2.37-2.444.60.46617821.01195.7
2.44-2.524.90.40417861.118196.1
2.52-2.614.90.37918091.093196.3
2.61-2.7150.30118011.21196.4
2.71-2.845.10.26718011.245197
2.84-2.995.20.24118631.35197.5
2.99-3.175.20.20418401.39197.7
3.17-3.425.30.15318561.384198
3.42-3.765.30.11318751.352198.5
3.76-4.35.30.10318851.629198.5
4.3-5.425.10.08517831.576191
5.42-305.10.06620431.503198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
Locallymodified Blu-Ice GUI interface to EPICS controldata collection
HKL-2000data reduction
PHENIX(phaser)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 3ODU

3odu


Resolution: 2.2→28.273 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8116 / SU ML: 0.26 / σ(F): 0 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1306 5.04 %RANDOM
Rwork0.218 ---
all0.2188 28455 --
obs0.2188 25921 91.01 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.432 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 224.91 Å2 / Biso mean: 46.5549 Å2 / Biso min: 19.34 Å2
Baniso -1Baniso -2Baniso -3
1-25.201 Å2-0 Å2-0 Å2
2---8.8018 Å20 Å2
3----16.3993 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 263 91 3824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083809
X-RAY DIFFRACTIONf_angle_d0.9485111
X-RAY DIFFRACTIONf_chiral_restr0.06586
X-RAY DIFFRACTIONf_plane_restr0.006611
X-RAY DIFFRACTIONf_dihedral_angle_d14.9651453
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1994-2.28740.38081100.31842190230075
2.2874-2.39150.31011360.28462533266985
2.3915-2.51750.26111410.25082627276889
2.5175-2.67510.23371330.23072721285492
2.6751-2.88140.24551650.21862761292693
2.8814-3.17110.27131590.22332850300995
3.1711-3.62910.25531430.21162922306597
3.6291-4.56920.20741610.1842894305596
4.5692-28.27550.18281580.20783117327597
Refinement TLS params.Method: refined / Origin x: -4.0967 Å / Origin y: -8.5829 Å / Origin z: 27.7598 Å
111213212223313233
T0.2563 Å20.0145 Å20.0126 Å2-0.2252 Å2-0.0069 Å2--0.2419 Å2
L0.1412 °20.0366 °20.0877 °2-0.1779 °2-0.1284 °2--0.1878 °2
S-0.0052 Å °0.0371 Å °-0.0278 Å °-0.0658 Å °0.0116 Å °0.0405 Å °0.0231 Å °0.0034 Å °-0.003 Å °
Refinement TLS groupSelection details: all

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