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- PDB-1nro: CRYSTALLOGRAPHIC STRUCTURES OF THROMBIN COMPLEXED WITH THROMBIN R... -

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Basic information

Entry
Database: PDB / ID: 1nro
TitleCRYSTALLOGRAPHIC STRUCTURES OF THROMBIN COMPLEXED WITH THROMBIN RECEPTOR PEPTIDES: EXISTENCE OF EXPECTED AND NOVEL BINDING MODES
Components
  • ALPHA-THROMBIN (LARGE SUBUNIT)
  • ALPHA-THROMBIN (SMALL SUBUNIT)
  • RECEPTOR BASED PEPTIDE NRP
KeywordsSERINE PROTEINASE/RECEPTOR / SERINE PROTEINASE-RECEPTOR complex
Function / homology
Function and homology information


negative regulation of renin secretion into blood stream / negative regulation of glomerular filtration / platelet dense granule organization / platelet dense tubular network / thrombin-activated receptor activity / establishment of synaptic specificity at neuromuscular junction / cell-cell junction maintenance / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / regulation of interleukin-1 beta production / connective tissue replacement involved in inflammatory response wound healing ...negative regulation of renin secretion into blood stream / negative regulation of glomerular filtration / platelet dense granule organization / platelet dense tubular network / thrombin-activated receptor activity / establishment of synaptic specificity at neuromuscular junction / cell-cell junction maintenance / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / regulation of interleukin-1 beta production / connective tissue replacement involved in inflammatory response wound healing / positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway / 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 / : / G-protein alpha-subunit binding / release of sequestered calcium ion into cytosol / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / cytolysis by host of symbiont cells / thrombin / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / G-protein beta-subunit binding / negative regulation of astrocyte differentiation / homeostasis of number of cells within a tissue / negative regulation of fibrinolysis / anatomical structure morphogenesis / regulation of sensory perception of pain / positive regulation of vasoconstriction / negative regulation of cytokine production involved in inflammatory response / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / G protein-coupled receptor activity / positive regulation of blood coagulation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Peptide ligand-binding receptors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of release of sequestered calcium ion into cytosol / Intrinsic Pathway of Fibrin Clot Formation / fibrinolysis / phospholipase C-activating G protein-coupled receptor signaling pathway / Thrombin signalling through proteinase activated receptors (PARs) / caveola / lipopolysaccharide binding / positive regulation of interleukin-8 production / Regulation of Complement cascade / neuromuscular junction / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of interleukin-6 production / negative regulation of proteolysis / growth factor activity / response to wounding / positive regulation of protein localization to nucleus / platelet activation / G alpha (q) signalling events / positive regulation of GTPase activity / Golgi lumen / activation of cysteine-type endopeptidase activity involved in apoptotic process / multicellular organism development / positive regulation of reactive oxygen species metabolic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / postsynaptic membrane / blood coagulation / late endosome / positive regulation of cytosolic calcium ion concentration / positive regulation of phosphatidylinositol 3-kinase signaling / heparin binding / positive regulation of MAPK cascade / positive regulation of I-kappaB kinase/NF-kappaB signaling / positive regulation of cell growth / response to lipopolysaccharide / collagen-containing extracellular matrix / regulation of cell shape / blood microparticle / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / early endosome / G protein-coupled receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / proteolysis / signaling receptor binding / serine-type endopeptidase activity / endoplasmic reticulum lumen
Similarity search - Function
Thrombin receptor / Protease-activated receptor / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain / Thrombin light chain domain superfamily / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / G-protein coupled receptors family 1 profile. ...Thrombin receptor / Protease-activated receptor / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain / Thrombin light chain domain superfamily / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / G-protein coupled receptors family 1 profile. / GPCR, rhodopsin-like, 7TM / Kringle domain / Kringle domain / Kringle / Kringle, conserved site / Kringle domain profile. / Kringle domain signature. / Kringle superfamily / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gla domain profile. / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gamma-carboxyglutamic acid-rich (GLA) domain / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / 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 / Resolution: 3.1 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, 1994-
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: ALPHA-THROMBIN (SMALL SUBUNIT)
H: ALPHA-THROMBIN (LARGE SUBUNIT)
R: RECEPTOR BASED PEPTIDE NRP


Theoretical massNumber of molelcules
Total (without water)37,2593
Polymers37,2593
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)128.100, 51.800, 62.900
Angle α, β, γ (deg.)90.00, 101.00, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO H 37
2: A FEW SIDE CHAINS IN BOTH THROMBIN AND RECEPTOR PEPTIDE DO NOT HAVE WELL-DEFINED ELECTRON DENSITY. THESE ATOMS HAVE BEEN GIVEN OCCUPANCIES OF 0.01 IN THIS ENTRY.

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Components

#1: Protein/peptide ALPHA-THROMBIN (SMALL SUBUNIT)


Mass: 4096.534 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00734, thrombin
#2: Protein ALPHA-THROMBIN (LARGE SUBUNIT)


Mass: 29780.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide RECEPTOR BASED PEPTIDE NRP


Mass: 3382.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P25116
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *R* IS USED FOR NRP.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
126 %(w/v)PEG80001reservoir
20.1 MTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.1 Å / % possible obs: 88 % / Rmerge F obs: 0.071

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 3.1→7 Å / σ(F): 2
Details: A FEW SIDE CHAINS IN BOTH THROMBIN AND RECEPTOR PEPTIDE DO NOT HAVE WELL-DEFINED ELECTRON DENSITY. THESE ATOMS HAVE BEEN GIVEN OCCUPANCIES OF 0.01 IN THIS ENTRY.
RfactorNum. reflection
obs0.171 4572
Refinement stepCycle: LAST / Resolution: 3.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 0 117 2481
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.025
X-RAY DIFFRACTIONp_angle_d0.0450.045
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.661.5
X-RAY DIFFRACTIONp_mcangle_it1.192
X-RAY DIFFRACTIONp_scbond_it0.932.5
X-RAY DIFFRACTIONp_scangle_it1.553
X-RAY DIFFRACTIONp_plane_restr0.0130.03
X-RAY DIFFRACTIONp_chiral_restr0.140.15
X-RAY DIFFRACTIONp_singtor_nbd0.260.5
X-RAY DIFFRACTIONp_multtor_nbd0.370.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.40.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor23
X-RAY DIFFRACTIONp_staggered_tor23.315
X-RAY DIFFRACTIONp_orthonormal_tor30.420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29 Å2

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