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(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE THROMBIN IN COMPLEX WITH THE EXTRACELLULAR FRAGMENT OF MURINE PAR4
 
Authors :  A. Bah, Z. Chen, L. A. Bush-Pelc, F. S. Mathews, E. Di Cera
Date :  09 May 07  (Deposition) - 10 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A (1x),B (1x),C (1x)
Keywords :  Serine Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bah, Z. Chen, L. A. Bush-Pelc, F. S. Mathews, E. Di Cera
Crystal Structures Of Murine Thrombin In Complex With The Extracellular Fragments Of Murine Protease-Activated Receptors Par3 And Par4.
Proc. Natl. Acad. Sci. Usa V. 104 11603 2007
PubMed-ID: 17606903  |  Reference-DOI: 10.1073/PNAS.0704409104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THROMBIN LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell: KIDNEY CELLS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Gene: F2, CF2
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - THROMBIN HEAVY CHAIN
    Chains: B
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell: KIDNEY CELLS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Gene: F2, CF2
    Mutation: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - PROTEINASE-ACTIVATED RECEPTOR 4
    Chains: C
    Engineered: YES
    Other Details: MIDWEST BIOTECH INC.
    Synonym: PAR-4, THROMBIN RECEPTOR-LIKE 3, COAGULATION FACTOR II RECEPTOR-LIKE 3
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (1x): A (1x)B (1x)C (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (0, 0)

(no "Site" information available for 2PV9)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:1 -B:122
2B:42 -B:58
3B:168 -B:182
4B:191 -B:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser B:36A-Pro B:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PV9)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.THRB_MOUSE361-615  1B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.THRB_MOUSE399-404  1B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.THRB_MOUSE559-570  1B:189-200
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.THRB_MOUSE361-615  1B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.THRB_MOUSE399-404  1B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.THRB_MOUSE559-570  1B:189-200
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.THRB_MOUSE361-615  1B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.THRB_MOUSE399-404  1B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.THRB_MOUSE559-570  1B:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 2PV9)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:43
 aligned with THRB_MOUSE | P19221 from UniProtKB/Swiss-Prot  Length:618

    Alignment length:43
                                   326       336       346       356   
          THRB_MOUSE    317 FHTFFNEKTFGLGEADCGLRPLFEKKSLKDTTEKELLDSYIDG  359
               SCOP domains ------------------------------------------- SCOP domains
               CATH domains 2pv9A00 A:1P-14M                            CATH domains
               Pfam domains Thrombin_light-2pv9A01 A:1P-14M             Pfam domains
         Sec.struct. author ............hhhhh..............hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------- Transcript
                2pv9 A   1P FHTFFNEKTFGLGEADCGLRPLFEKKSLKDTTEKELLDSYIDG  14M
                            ||||||||1G||||||   4        14|||||||14J|||
                           1P|||||||1G||||||            14A||||||14J|||
                            1O|||||||1F|||||             14B||||||14K||
                             1N|||||| 1E||||              14C||||||14L|
                              1M|||||  1D|||               14D||||| 14M
                               1L||||   1C||                14E||||    
                                1K|||    1B|                 14F|||    
                                 1J||     1A                  14G||    
                                  1I|                          14H|    
                                   1H                           14I    


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with THRB_MOUSE | P19221 from UniProtKB/Swiss-Prot  Length:618

    Alignment length:258
                                   370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610        
          THRB_MOUSE    361 IVEGWDAEKGIAPWQVMLFRKSPQELLCGASLISDRWVLTAAHCILYPPWDKNFTENDLLVRIGKHSRTRYERNVEKISMLEKIYVHPRYNWRENLDRDIALLKLKKPVPFSDYIHPVCLPDKQTVTSLLRAGYKGRVTGWGNLRETWTTNINEIQPSVLQVVNLPIVERPVCKASTRIRITDNMFCAGFKVNDTKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRKGKYGFYTHVFRLKRWIQKVIDQFG  618
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2pv9B01     2pv9B02 B:28-120,B:233-245 Trypsin-like serine proteases                                                 2pv9B01 B:16-27,B:121-232 Trypsin-like serine proteases                                                                        2pv9B02      - CATH domains
               Pfam domains Trypsin-2pv9B01 B:16-238                                                                                                                                                                                                                                  -------- Pfam domains
         Sec.struct. author ....ee.........eeeee....eeeeeeee....eeeehhhh.eehhhhee.....eeeee.............eeeeeeeeee..............eeeee................hhhhhhhhh....eeeeee....................eeeeee..hhhhhhhh........eeee...................eeeee......eeeeeeeeee.........eeeeehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 361-615                                                                                                                                                                                                                    --- PROSITE (1)
                PROSITE (2) --------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2pv9 B   16 IVEGWDAEKGIAPWQVMLFRKSPQELLCGASLISDRWVLTAAHCILYPPWDKNFTENDLLVRIGKHSRTRYERNVEKISMLEKIYVHPRYNWRENLDRDIALLKLKKPVPFSDYIHPVCLPDKQTVTSLLRAGYKGRVTGWGNLRETWTTNINEIQPSVLQVVNLPIVERPVCKASTRIRITDNMFCAGFKVNDTKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRKGKYGFYTHVFRLKRWIQKVIDQFG  246
                                    25        35 |      44        54      |60D|||||   65        75  |     84        94   |   103       113       123      |130       140      149A||||   155       165       175      184A  |||| 190       200    || 208       219  |    228       238        
                                               36A                      60A||||||||               77A                  97A                             129A||                 149A||||                                184A  ||||               204A|          217|  |                         
                                                                         60B|||||||                                                                     129B|                  149B|||                                   186A|||                204B           219  |                         
                                                                          60C||||||                                                                      129C                   149C||                                    186B||                                 221A                         
                                                                           60D|||||                                                                                              149D|                                     186C|                                                              
                                                                            60E||||                                                                                               149E                                      186D                                                              
                                                                             60F|||                                                                                                                                                                                                           
                                                                              60G||                                                                                                                                                                                                           
                                                                               60H|                                                                                                                                                                                                           
                                                                                60I                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:26
 aligned with PAR4_MOUSE | O88634 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:26
                                    60        70      
          PAR4_MOUSE     51 KSSDKPNPRGYPGKFCANDSDTLELP   76
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author .......................... Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                2pv9 C   51 KSSDKPNPRGYPGKFCANDSDTLELP   76
                                    60        70
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2PV9)

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Peptidase_PA (797)
(-)
Clan: no clan defined [family: Thrombin_light] (136)

(-) Gene Ontology  (47, 51)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (THRB_MOUSE | P19221)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0070053    thrombospondin receptor activity    Combining with thrombospondin and transmitting the signal to initiate a change in cell activity.
biological process
    GO:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0071260    cellular response to mechanical stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0048712    negative regulation of astrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of astrocyte differentiation.
    GO:0045861    negative regulation of proteolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0030194    positive regulation of blood coagulation    Any process that activates or increases the frequency, rate or extent of blood coagulation.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0032967    positive regulation of collagen biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:1900738    positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of phospholipase C-activating G-protein coupled receptor signaling pathway.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:2000379    positive regulation of reactive oxygen species metabolic process    Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process.
    GO:0051281    positive regulation of release of sequestered calcium ion into cytosol    Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051480    regulation of cytosolic calcium ion concentration    Any process involved in the maintenance of an internal steady state of calcium ions within the cytosol of a cell or between the cytosol and its surroundings.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0014854    response to inactivity    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inactivity stimulus.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
    GO:0070493    thrombin-activated receptor signaling pathway    The series of molecular signals generated as a consequence of a thrombin-activated receptor binding to one of its physiological ligands.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Chain C   (PAR4_MOUSE | O88634)
molecular function
    GO:0004930    G-protein coupled receptor activity    Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0015057    thrombin-activated receptor activity    A G-protein-coupled receptor activity that is activated by cleavage by thrombin, which exposes a tethered ligand corresponding to the new N-terminus, which binds to the receptor and activates it.
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0051281    positive regulation of release of sequestered calcium ion into cytosol    Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0070493    thrombin-activated receptor signaling pathway    The series of molecular signals generated as a consequence of a thrombin-activated receptor binding to one of its physiological ligands.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  PAR4_MOUSE | O88634
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  THRB_MOUSE | P19221
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        THRB_MOUSE | P19221: 2ocv 2pux 3edx 3hk3 3hk6 3hki

(-) Related Entries Specified in the PDB File

1shh SLOW FORM OF THROMBIN BOUND WITH PPACK
2ocv STRUCTURAL BASIS OF NA+ ACTIVATION MIMICRY IN MURINE THROMBIN
2pux