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- PDB-4dy7: Crystal structures of protease nexin-1 in complex with S195A thrombin -

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Basic information

Entry
Database: PDB / ID: 4dy7
TitleCrystal structures of protease nexin-1 in complex with S195A thrombin
Components
  • Glia-derived nexin
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serpin / protease / heparin / cell surface / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cerebellar granular layer morphogenesis / mating plug formation / seminal vesicle epithelium development / regulation of timing of cell differentiation / secretory granule organization / negative regulation of sodium ion transport / detection of mechanical stimulus involved in sensory perception / secretion by cell / negative regulation of blood coagulation / positive regulation of astrocyte differentiation ...cerebellar granular layer morphogenesis / mating plug formation / seminal vesicle epithelium development / regulation of timing of cell differentiation / secretory granule organization / negative regulation of sodium ion transport / detection of mechanical stimulus involved in sensory perception / secretion by cell / negative regulation of blood coagulation / positive regulation of astrocyte differentiation / innervation / platelet alpha granule / negative regulation of platelet aggregation / negative regulation of plasminogen activation / glycosaminoglycan binding / Dissolution of Fibrin Clot / negative regulation of protein processing / 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of smoothened signaling pathway / 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 / regulation of cell migration / regulation of synaptic transmission, glutamatergic / 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 / long-term synaptic potentiation / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / protein catabolic process / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / neuromuscular junction / serine-type endopeptidase inhibitor activity / negative regulation of protein catabolic process / positive regulation of insulin secretion / negative regulation of cell growth / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / cell differentiation / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / negative regulation of cell population proliferation / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol
Similarity search - Function
Epsilon-Thrombin; Chain L / Thrombin light chain domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family ...Epsilon-Thrombin; Chain L / Thrombin light chain domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 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 / Few Secondary Structures / Irregular / 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 / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Prothrombin / Glia-derived nexin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuntington, J.A. / Li, W.
CitationJournal: Blood / Year: 2012
Title: Crystal structures of protease nexin-1 in complex with heparin and thrombin suggest a 2-step recognition mechanism.
Authors: Li, W. / Huntington, J.A.
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombin light chain
B: Thrombin heavy chain
C: Glia-derived nexin
D: Thrombin light chain
E: Thrombin heavy chain
F: Glia-derived nexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,92212
Polymers154,6426
Non-polymers2806
Water1,982110
1
A: Thrombin light chain
B: Thrombin heavy chain
C: Glia-derived nexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5618
Polymers77,3213
Non-polymers2405
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-47 kcal/mol
Surface area26440 Å2
MethodPISA
2
D: Thrombin light chain
E: Thrombin heavy chain
F: Glia-derived nexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3614
Polymers77,3213
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-29 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.960, 86.670, 101.890
Angle α, β, γ (deg.)90.00, 94.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
12
13
/ NCS ensembles :
ID
1
2
3
DetailsChains A and B make up thrombin complexed to protease nexin-1 in chain C, and represents the initial heparin-bridged complex. / Chains D and E make up thrombin complexed with protease nexin-1 of chain F. This represents the productive Michaelis complex.

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Components

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Protein/peptide , 1 types, 2 molecules AD

#1: Protein/peptide Thrombin light chain /


Mass: 5641.175 Da / Num. of mol.: 2 / Fragment: UNP residues 315-363 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell (production host): BABY HAMSTER KIDNEY (BHK) CELLS / Organ (production host): KIDNEY / Production host: CRICETINAE GEN. SP. (mammal) / References: UniProt: P00734, thrombin

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Protein , 2 types, 4 molecules BECF

#2: Protein Thrombin heavy chain /


Mass: 29764.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell (production host): BABY HAMSTER KIDNEY (BHK) CELLS / Organ (production host): KIDNEY / Production host: CRICETINAE GEN. SP. (mammal) / References: UniProt: P00734, thrombin
#3: Protein Glia-derived nexin / GDN / Peptidase inhibitor 7 / PI-7 / Protease nexin 1 / PN-1 / Protease nexin I / Serpin E2


Mass: 41915.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE2, PI7, PN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07093

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Non-polymers , 4 types, 116 molecules

#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.4
Details: 0.14M calcium acetate, 13% PEG3350, pH 7.4, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2008
RadiationMonochromator: Si111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.8→51.37 Å / Num. all: 41246 / Num. obs: 39308 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0098refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.04 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 35.742 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1956 5 %RANDOM
Rwork0.223 ---
obs0.225 37320 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å2-0 Å24.2 Å2
2---4.55 Å2-0 Å2
3---6.9 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9831 0 15 110 9956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.02210093
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.5561.95613781
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.91551332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02524.085377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.798151447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4041547
X-RAY DIFFRACTIONr_chiral_restr0.0380.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0217695
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 142 -
Rwork0.346 2680 -
obs--96.15 %

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