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

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Basic information

Entry
Database: PDB / ID: 1nrp
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 NR'S
KeywordsSERINE PROTEINASE/RECEPTOR / SERINE PROTEINASE-RECEPTOR complex
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 vasoconstriction / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / 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 / G-protein alpha-subunit binding / anatomical structure morphogenesis / positive regulation of blood coagulation / negative regulation of fibrinolysis / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / 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 / response to wounding / positive regulation of interleukin-6 production / 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 / Protease-activated receptor / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site ...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. / 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 / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / Trypsin / 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 / Resolution: 3 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 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 2.1Oct 23, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / pdbx_validate_symm_contact
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,8033
Polymers36,8033
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-17 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.300, 51.100, 63.000
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
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.
Components on special symmetry positions
IDModelComponents
11L-432-

HOH

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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 NR'S


Mass: 2926.152 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


Mass: 18.015 Da / Num. of mol.: 73 / 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 NR'S.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.46 %
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: 3 Å / % possible obs: 88 % / Rmerge F obs: 0.092

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 3→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
obs0.199 5696
Refinement stepCycle: LAST / Resolution: 3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 0 73 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.057
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.581
X-RAY DIFFRACTIONp_mcangle_it1.081.5
X-RAY DIFFRACTIONp_scbond_it12
X-RAY DIFFRACTIONp_scangle_it1.682.5
X-RAY DIFFRACTIONp_plane_restr0.0230.04
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_nbd0.360.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.13
X-RAY DIFFRACTIONp_staggered_tor25.515
X-RAY DIFFRACTIONp_orthonormal_tor34.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34 Å2

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