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- PDB-1nrr: Crystallographic structures of Thrombin complexed with Thrombin r... -

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Basic information

Entry
Database: PDB / ID: 1nrr
TitleCrystallographic structures of Thrombin complexed with Thrombin receptor peptides: Existence of expected and novel binding modes
Components
  • Proteinase-activated receptor 1
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHydrolase/HYDROLASE INHIBITOR / Hydrolase-Hydrolase Inhibitor complex / BLOOD CLOTTING
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
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Prothrombin / Proteinase-activated receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsTulinsky, A. / Mathews, I.I.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and novel binding modes.
Authors: Mathews, I.I. / Padmanabhan, K.P. / Ganesh, V. / Tulinsky, A. / Ishii, M. / Chen, J. / Turck, C.W. / Coughlin, S.R. / Fenton 2nd., J.W.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Structure of the Hirudin-Thrombin Complex
Authors: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin
Authors: Skrzypczak-Jankun, E. / Carperos, V.E. / Ravichandran, K.G. / Tulinsky, A. / Westbrook, M. / Maraganore, J.M.
History
DepositionJan 18, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _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
L: Thrombin light chain
H: Thrombin heavy chain
R: Proteinase-activated receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6744
Polymers36,2203
Non-polymers4541
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.300, 72.200, 72.300
Angle α, β, γ (deg.)90.00, 100.00, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO H 37
Components on special symmetry positions
IDModelComponents
11H-570-

HOH

21H-638-

HOH

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Components

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


Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: RESIDUES 328-363 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#2: Protein Thrombin heavy chain / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 364-622 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide Proteinase-activated receptor 1 / Thrombin receptor / Coagulation factor II receptor


Mass: 2343.501 Da / Num. of mol.: 1 / Fragment: UNP residues 43-60 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25116
#4: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / References: D-Phe-Pro-Arg-CH2Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE- ...THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 57
Sequence detailsCHYMOTRYPSIN NUMBERING SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF ...CHYMOTRYPSIN NUMBERING SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, EMBO J. 8, 3467-3475). THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *R* IS USED FOR XA.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8.5 / PH range high: 6.5
Components of the solutions
*PLUS
Conc.: 24-30 %(w/v) / Common name: PEG4000 / Details: or PEG8000

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / % possible obs: 91 % / Rmerge F obs: 0.035

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→7 Å / σ(F): 2 /
RfactorNum. reflection
obs0.145 12963
Refinement stepCycle: LAST / Resolution: 2.4→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2271 0 30 207 2508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.025
X-RAY DIFFRACTIONp_angle_d0.0440.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.911
X-RAY DIFFRACTIONp_mcangle_it1.581.5
X-RAY DIFFRACTIONp_scbond_it2.242
X-RAY DIFFRACTIONp_scangle_it3.372.5
X-RAY DIFFRACTIONp_plane_restr0.0250.03
X-RAY DIFFRACTIONp_chiral_restr0.170.15
X-RAY DIFFRACTIONp_singtor_nbd0.20.5
X-RAY DIFFRACTIONp_multtor_nbd0.250.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.230.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.83
X-RAY DIFFRACTIONp_staggered_tor20.515
X-RAY DIFFRACTIONp_orthonormal_tor30.720
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25 Å2

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