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- PDB-3jz2: Crystal structure of human thrombin mutant N143P in E* form -

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Basic information

Entry
Database: PDB / ID: 3jz2
TitleCrystal structure of human thrombin mutant N143P in E* form
Components
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE / Serine protease / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Gamma-carboxyglutamic acid / Glycoprotein / Kringle / Protease / Secreted / Zymogen
Function / homology
Function and homology information


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 ...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) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / 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 / 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 / acute-phase response / Regulation of Complement cascade / 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 / 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) / positive regulation of reactive oxygen species metabolic process / blood coagulation / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
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. ...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 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNiu, W. / Chen, Z. / Bush-Pelc, L.A. / Bah, A. / Gandhi, P.S. / Di Cera, E.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Mutant N143P reveals how Na+ activates thrombin
Authors: Niu, W. / Chen, Z. / Bush-Pelc, L.A. / Bah, A. / Gandhi, P.S. / Di Cera, E.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural identification of the pathway of long-range communication in an allosteric enzyme
Authors: Gandhi, P.S. / Chen, Z. / Mathews, F.S. / Di Cera, E.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Molecular dissection of Na+ binding to thrombin
Authors: Pineda, A.O. / Carrell, C.J. / Bush, L.A. / Prasad, S. / Caccia, S. / Chen, Z. / Mathews, F.S. / Di Cera, E.
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4497
Polymers33,8602
Non-polymers5905
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-7 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.890, 57.890, 119.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein/peptide Thrombin light chain


Mass: 4096.534 Da / Num. of mol.: 1 / Mutation: N143P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin
#2: Protein Thrombin heavy chain


Mass: 29763.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M imidazole and 7% PEG 8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2009
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 15452 / Num. obs: 14942 / % possible obs: 96.7 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.2 / Num. unique all: 595 / % possible all: 77.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPfrom CCP4phasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PEB entry 3BEI

3bei


Resolution: 2.4→25.3 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 15.999 / SU ML: 0.171 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R: 0.338 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24649 747 5 %RANDOM
Rwork0.18906 ---
obs0.19194 14167 96.84 %-
all-14629 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.721 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 38 116 2388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222318
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9763122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67723.148108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76415406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3191520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211754
X-RAY DIFFRACTIONr_mcbond_it0.6571.51364
X-RAY DIFFRACTIONr_mcangle_it1.25122197
X-RAY DIFFRACTIONr_scbond_it1.7823954
X-RAY DIFFRACTIONr_scangle_it2.9494.5925
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 48 -
Rwork0.3 851 -
obs--78.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.77232.1533-2.91879.3563-2.04635.2063-0.1189-0.1102-0.2285-0.3399-0.0551-0.68770.23890.24770.1740.21080.0191-0.07760.1655-0.07890.265115.96553.791-9.9923
23.012-1.25090.25129.3923-1.21122.208-0.0110.1305-0.4044-0.40960.0350.48930.2083-0.3074-0.02410.0943-0.051-0.06260.1246-0.01720.1156.17064.8887-10.6939
31.68360.81910.24522.45640.60371.88110.0071-0.2319-0.04540.25950.0502-0.07230.243-0.0742-0.05730.07670.0103-0.00410.09980.01650.063119.656512.63457.5358
41.38421.6910.04873.97720.6391.933-0.0113-0.273-0.0290.27250.0223-0.05750.1256-0.1241-0.01090.18490.0323-0.03770.17370.05280.10218.65844.175711.1441
52.1731.4830.59765.52040.31862.89090.0424-0.1943-0.09160.15970.0767-0.4249-0.00520.2849-0.11910.0350.02740.00980.1091-0.01540.063528.061513.3533.8828
62.6772.812-1.08364.6051-1.64432.3917-0.18040.28550.028-0.40220.23420.00750.0987-0.0042-0.05370.2054-0.0304-0.010.140.01760.042221.946719.0259-14.6506
71.89841.04510.98366.31190.84711.39480.0231-0.13960.18110.46230.08920.1849-0.3035-0.1286-0.11220.20660.0660.04430.1214-0.03720.126812.077624.4083-0.3828
89.16742.76551.69994.80491.20822.48650.298-0.29281.0050.3034-0.2840.4867-0.4444-0.4912-0.0140.24270.05930.06530.1317-0.00550.182814.931630.4184-2.776
90.73521.31340.180510.70026.61794.87080.0124-0.27930.4103-0.956-0.49121.1446-0.8789-0.26960.47880.49690.3276-0.11440.6795-0.2570.3896.34824.43033.5146
101.4515-0.04961.30922.16741.70135.3733-0.0510.02690.062-0.1466-0.00240.0492-0.10860.07420.05350.0842-0.01010.00830.06490.00730.059216.778416.6941-5.2913
111.3774-1.20532.72069.6686-6.05646.9423-0.2466-0.39960.16511.00510.30270.7494-0.8392-0.7722-0.05610.48780.11940.14710.3971-0.09180.268810.094630.44056.7321
123.80540.2887-2.44554.3172-0.18273.73930.05320.09730.1492-0.2749-0.0483-0.731-0.03250.4002-0.00490.0808-0.00160.03720.1582-0.0090.174729.924718.7533-4.4102
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 14
3X-RAY DIFFRACTION3B16 - 60
4X-RAY DIFFRACTION4B61 - 82
5X-RAY DIFFRACTION5B83 - 121
6X-RAY DIFFRACTION6B122 - 130
7X-RAY DIFFRACTION7B131 - 175
8X-RAY DIFFRACTION8B176 - 186
9X-RAY DIFFRACTION9B187 - 193
10X-RAY DIFFRACTION10B194 - 217
11X-RAY DIFFRACTION11B219 - 225
12X-RAY DIFFRACTION12B226 - 245

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