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- PDB-1de7: INTERACTION OF FACTOR XIII ACTIVATION PEPTIDE WITH ALPHA-THROMBIN... -

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Basic information

Entry
Database: PDB / ID: 1de7
TitleINTERACTION OF FACTOR XIII ACTIVATION PEPTIDE WITH ALPHA-THROMBIN: CRYSTAL STRUCTURE OF THE ENZYME-SUBSTRATE COMPLEX
Components
  • ALPHA-THROMBIN (HEAVY CHAIN)
  • ALPHA-THROMBIN (LIGHT CHAIN)
  • FACTOR XIII ACTIVATION PEPTIDE (28-37)
KeywordsHYDROLASE/HYDROLASE SUBSTRATE / ENZYME-SUBSTRATE COMPLEX / ALPHA-THROMBIN / FACTOR XIII ACTIVATION PEPTIDE / HYDROLASE/PEPTIDE / BLOOD CLOTTING / HYDROLASE-HYDROLASE SUBSTRATE complex
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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / 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 / 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 / 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 / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / 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) / 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 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 / 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
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 Å
AuthorsSadasivan, C. / Yee, V.C.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Interaction of the factor XIII activation peptide with alpha -thrombin. Crystal structure of its enzyme-substrate analog complex.
Authors: Sadasivan, C. / Yee, V.C.
#1: Journal: Protein Sci. / Year: 1992
Title: The Refined 1.9 Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed ...Title: The Refined 1.9 Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships
Authors: Bode, W. / Turk, D. / Karshikov, A.
#2: Journal: Eur.J.Biochem. / Year: 1992
Title: The Interaction of Thrombin with Fibrinogen: A Structural Basis for its Specificity
Authors: Stubbs, M.T. / Oschkinat, H. / Mayer, I. / Huber, R. / Angliker, H. / Stoner, S.R. / Bode, W.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Three-Dimensional Structure of a Transglutaminase: Human Blood Coagulation Factor Xiii
Authors: Yee, V.C. / Pedersen, L.C. / Trong, I.L. / Bishop, P.D. / Stenkamp, R.E. / Teller, D.C.
History
DepositionNov 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Aug 9, 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_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ALPHA-THROMBIN (LIGHT CHAIN)
H: ALPHA-THROMBIN (HEAVY CHAIN)
J: ALPHA-THROMBIN (LIGHT CHAIN)
K: ALPHA-THROMBIN (HEAVY CHAIN)
A: FACTOR XIII ACTIVATION PEPTIDE (28-37)
B: FACTOR XIII ACTIVATION PEPTIDE (28-37)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0658
Polymers70,0196
Non-polymers462
Water8,629479
1
L: ALPHA-THROMBIN (LIGHT CHAIN)
H: ALPHA-THROMBIN (HEAVY CHAIN)
A: FACTOR XIII ACTIVATION PEPTIDE (28-37)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0334
Polymers35,0103
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-29 kcal/mol
Surface area12690 Å2
MethodPISA, PQS
2
J: ALPHA-THROMBIN (LIGHT CHAIN)
K: ALPHA-THROMBIN (HEAVY CHAIN)
B: FACTOR XIII ACTIVATION PEPTIDE (28-37)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0334
Polymers35,0103
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-29 kcal/mol
Surface area12260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.070, 81.260, 85.460
Angle α, β, γ (deg.)90.00, 101.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHERE ARE TWO INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT: COMPLEX 1 ALPHA-THROMBIN: CHAINS L, H FACTOR XIII PEPTIDE: CHAIN A COMPLEX 2 ALPHA-THROMBIN: CHAINS J, K FACTOR XIII PEPTIDE: CHAIN B

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Components

#1: Protein/peptide ALPHA-THROMBIN (LIGHT CHAIN)


Mass: 4096.534 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P00734, thrombin
#2: Protein ALPHA-THROMBIN (HEAVY CHAIN)


Mass: 29780.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P00734, thrombin
#3: Protein/peptide FACTOR XIII ACTIVATION PEPTIDE (28-37)


Mass: 1132.761 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE FACTOR XIII DERIVED PEPTIDE CONTAIN A C-TERMINAL CHLOROMETHYLKETONE GROUP AND IS COVALENTLY ...THE FACTOR XIII DERIVED PEPTIDE CONTAIN A C-TERMINAL CHLOROMETHYLKETONE GROUP AND IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES OF THROMBIN. THE UNBOUND FORM OF THE PEPTIDE IS THR-VAL-GLU-LEU-GLN-GLY-VAL-VAL-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) VIA A HEMIKETAL GROUP TO OG SER H 195; 2) VIA A METHYLENE GROUP TO NE2 HIS H 57.
Sequence detailsCHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED FOR THROMBIN, BASED ON THE ...CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED FOR THROMBIN, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (W.BODE ET AL., 1989, EMBO J. 4 8, 3467-3475). PEPTIDE NUMBERING IS BASED ON THE CORRESPONDING RESIDUES IN FACTOR XIII

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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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growpH: 5.5 / Details: PEG8000, SODIUM CHLORIDE, SODIUM CITRATE, pH 5.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
32 %PEG80001reservoir
4200 mMsodium chloride1reservoir
550 mMsodium citrate1reservoir
2peptide1drop10-fold molar excess in water

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 10, 1998 / Details: YALE MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 45245 / % possible obs: 91.8 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 22
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.157 / % possible all: 79.3
Reflection
*PLUS
Num. measured all: 124210
Reflection shell
*PLUS
% possible obs: 79.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THROMBIN CRYSTAL STRUCTURE WITH PDB ID 1AHT

1aht


Resolution: 2→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2226 5 %RANDOM
Rwork0.194 ---
obs0.194 44341 90 %-
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 2 479 5114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.46
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3069 --
Rwork0.2718 4466 -
obs--78.4 %
Xplor fileSerial no: 1 / Param file: PARAM19.PRO / Topol file: TOPH19.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.75
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.64

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