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- PDB-3gis: Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin -

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Basic information

Entry
Database: PDB / ID: 3gis
TitleCrystal Structure of Na-free Thrombin in Complex with Thrombomodulin
Components
  • (Prothrombin) x 2
  • Thrombomodulin
KeywordsBLOOD CLOTTING / protein-protein complex / coagulation / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Gamma-carboxyglutamic acid / Glycoprotein / Hydrolase / Kringle / Protease / Secreted / Serine protease / Zymogen / EGF-like domain / Hydroxylation / Membrane / Receptor / Thrombophilia / Transmembrane
Function / homology
Function and homology information


blood coagulation, common pathway / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway ...blood coagulation, common pathway / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / 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 / positive regulation of blood coagulation / negative regulation of fibrinolysis / response to cAMP / response to X-ray / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / regulation of cytosolic calcium ion concentration / 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 / negative regulation of cytokine production involved in inflammatory response / 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 receptor signaling pathway via JAK-STAT / growth factor activity / lipopolysaccharide binding / female pregnancy / positive regulation of insulin secretion / platelet activation / response to wounding / 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 / transmembrane signaling receptor activity / signaling receptor activity / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / : / positive regulation of cell growth / response to lipopolysaccharide / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / external side of plasma membrane / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombomodulin-like, EGF-like / : / Thrombomodulin like fifth domain, EGF-like / Thrombomodulin-like domain / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / : / Calcium-binding EGF domain ...Thrombomodulin-like, EGF-like / : / Thrombomodulin like fifth domain, EGF-like / Thrombomodulin-like domain / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / : / Calcium-binding EGF domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Laminin / Laminin / C-type lectin-like/link domain superfamily / Coagulation Factor Xa inhibitory site / C-type lectin fold / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / EGF-like calcium-binding domain / Calcium-binding EGF-like 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 / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Ribbon / Few Secondary Structures / Irregular / 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 / 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 / Thrombomodulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsAdams, T.E. / Huntington, J.A.
CitationJournal: J.Thromb.Haemost. / Year: 2009
Title: Molecular basis of thrombomodulin activation of slow thrombin
Authors: Adams, T.E. / Li, W. / Huntington, J.A.
History
DepositionMar 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 17, 2016Group: Other
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prothrombin
B: Prothrombin
C: Prothrombin
D: Prothrombin
E: Prothrombin
F: Prothrombin
X: Thrombomodulin
Y: Thrombomodulin
Z: Thrombomodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,57127
Polymers145,0109
Non-polymers1,56118
Water10,359575
1
A: Prothrombin
B: Prothrombin
X: Thrombomodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,04911
Polymers48,3373
Non-polymers7138
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-100 kcal/mol
Surface area13600 Å2
2
C: Prothrombin
D: Prothrombin
Y: Thrombomodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8579
Polymers48,3373
Non-polymers5206
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-62 kcal/mol
Surface area13510 Å2
3
E: Prothrombin
F: Prothrombin
Z: Thrombomodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6657
Polymers48,3373
Non-polymers3284
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-50 kcal/mol
Surface area13140 Å2
Unit cell
Length a, b, c (Å)66.250, 100.340, 229.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 3 molecules ACE

#1: Protein/peptide Prothrombin / Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin ...Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin light chain / Thrombin heavy chain


Mass: 5641.175 Da / Num. of mol.: 3 / Fragment: Thrombin light-chain, UNP residues 315-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3)pLysS / References: UniProt: P00734, thrombin

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Protein , 2 types, 6 molecules BDFXYZ

#2: Protein Prothrombin / Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin ...Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin light chain / Thrombin heavy chain


Mass: 29764.219 Da / Num. of mol.: 3 / Fragment: Thrombin heavy-chain, UNP residues 364-622 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3)pLysS / References: UniProt: P00734, thrombin
#3: Protein Thrombomodulin / TM / Fetomodulin


Mass: 12931.283 Da / Num. of mol.: 3
Fragment: Thrombomodulin EGF domains 4-5-6, UNP residues 363-483
Mutation: M388L,R456G,H457Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THBD, THRM / Plasmid: pET39b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07204

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Non-polymers , 3 types, 593 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2007 / Details: mirrors
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→91.9 Å / Num. all: 60765 / Num. obs: 58334 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.5 / % possible all: 95

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JOU, 1DX5

1jou

1dx5


Resolution: 2.4→40 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2875 4.7 %RANDOM
Rwork0.211 ---
all0.247 60715 --
obs0.243 57399 94.5 %-
Solvent computationBsol: 21.479 Å2
Displacement parametersBiso max: 124.81 Å2 / Biso mean: 28.213 Å2 / Biso min: 2.83 Å2
Baniso -1Baniso -2Baniso -3
1-4.64 Å20 Å20 Å2
2---6.867 Å20 Å2
3---2.227 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9539 0 78 575 10192
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.347
X-RAY DIFFRACTIONc_mcbond_it1.3171.5
X-RAY DIFFRACTIONc_scbond_it1.9992
X-RAY DIFFRACTIONc_mcangle_it2.1732
X-RAY DIFFRACTIONc_scangle_it2.9562.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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