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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMANIZED FAB FRAGMENT OF ANTI-TISSUE-FACTOR ANTIBODY IN COMPLEX WITH TISSUE FACTOR
 
Authors :  U. Ohto, R. Mizutani, M. Nakamura, H. Adachi, Y. Satow
Date :  25 Jul 03  (Deposition) - 25 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Tissue Factor, Antigen, Antibody, Fab, Immune System/Blood Clotting Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  U. Ohto, R. Mizutani, M. Nakamura, H. Adachi, Y. Satow
Crystal Structure Of A Humanized Fab Fragment Of Anti-Tissue-Factor Antibody In Complex With Tissue Factor.
J. Synchrotron Radiat. V. 11 105 2004
PubMed-ID: 14646147
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG FAB LIGHT CHAIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentANTI-TISSUE-FACTOR ANTIBODY HATR-5 FAB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - IGG FAB HEAVY CHAIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentANTI-TISSUE-FACTOR ANTIBODY HATR-5 FAB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - TISSUE FACTOR
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 606-810
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTF, COAGULATION FACTOR III, THROMBOPLASTIN, CD142 ANTIGEN, BLOOD COAGULATION FACTOR

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1UJ3)

(-) Sites  (0, 0)

(no "Site" information available for 1UJ3)

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3A:214 -B:431
4B:322 -B:396
5B:444 -B:500
6C:649 -C:657
7C:786 -C:809

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Ser A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:450 -Pro B:451
5Glu B:452 -Pro B:453
6Glu C:626 -Pro C:627

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014299I145VTF_HUMANPolymorphism3917627CI713V
2UniProtVAR_012008R163WTF_HUMANPolymorphism5901CR731W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TISSUE_FACTORPS00621 Tissue factor signature.TF_HUMAN77-94  1C:645-662

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003340471aENSE00001452073chr1:95007356-95007093264TF_HUMAN1-34340--
1.3ENST000003340473ENSE00000777349chr1:95005924-95005813112TF_HUMAN34-71381C:606-63934
1.4ENST000003340474ENSE00001329748chr1:95001720-95001521200TF_HUMAN71-138681C:639-70668
1.5bENST000003340475bENSE00000777351chr1:94998824-94998646179TF_HUMAN138-197601C:706-76560
1.6ENST000003340476ENSE00000777352chr1:94998036-94997877160TF_HUMAN198-251541C:766-81045
1.7bENST000003340477bENSE00001906129chr1:94996152-949947811372TF_HUMAN251-295450--

(-) Sequences/Alignments

Asymmetric/Biological 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:214
                                                                                                                                                                                                                                                      
               SCOP domains d1uj3a1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1uj3a2 A:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1uj3A01 A:1-108 Immunoglobulins                                                                             1uj3A02 A:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uj3 A   1 DIQMTQSPSSLSASVGDRVTITCKASQDIKSFLSWYQQKPEKAPKSLIYYATSLADGVPSRFSGSGSGTDYTLTISSLQPEDFATYYCLQHGESPYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    

Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1uj3b1 B:301-417 Immunoglobulin heavy chain variable domain, VH                                                     d1uj3b2 B:418-517 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1uj3B01 B:301-417 Immunoglobulins                                                                                    1uj3B02 B:418-517 Immunoglobulins                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uj3 B 301 QVQLLESGAVLARPGTSVKISCKASGFNIKDYYMHWVKQRPGQGLEWIGGNDPANGHSMYDPKFQGRVTITADTSTSTVFMELSSLRSEDTAVYYCARDSGYAMDYWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVES 517
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       

Chain C from PDB  Type:PROTEIN  Length:205
 aligned with TF_HUMAN | P13726 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:205
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237     
             TF_HUMAN    38 TVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIVKDVKQTYLARVFSYPAGNVESTGSAGEPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVDKGENYCFSVQAVIPSRTVNRKSTDSPVECM 242
               SCOP domains d1uj3c1 C:606-706 Extracellular region of human tissue factor                                        d1uj3c2 C:707-810 Extracellular region of human tissue factor                                            SCOP domains
               CATH domains 1uj3C01 C:606-705 Immunoglobulins                                                                   1uj3C02 C:706-810 Immunoglobulins                                                                         CATH domains
               Pfam domains Tissue_fac-1uj3C02 C:606-686                                                     -------------------Interfer-bind-1uj3C01 C:706-810                                                                           Pfam domains
         Sec.struct. author ....eeeeeeee..eeeeeee.....eeeeeeee.....eeeeeeee...eeehhhhhh.......eeeeeeee.....................hhhhhh......eeeeeee..eeeeee...eeeeee..eeeehhhhhhhhheeeeeeee.....eeeeee...eeee.......eeeeeeee...............ee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------V-----------------W------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------TISSUE_FACTOR     ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: C:606-639          ------------------------------------------------------------------Exon 1.5b  PDB: C:706-765 UniProt: 138-197                  Exon 1.6  PDB: C:766-810 UniProt: 198-251     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.4  PDB: C:639-706 UniProt: 71-138                            -------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1uj3 C 606 TVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIVKDVKQTYLARVFSYPAGNVESTGSAGEPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVDKGENYCFSVQAVIPSRTVNRKSTDSPVECM 810
                                   615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805     

   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  (5, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
1a1uj3A02A:109-211
1b1uj3B02B:418-517
1c1uj3C01C:606-705
1d1uj3C02C:706-810
1e1uj3B01B:301-417
1f1uj3A01A:1-108

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (TF_HUMAN | P13726)
molecular function
    GO:0004896    cytokine receptor activity    Combining with a cytokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    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).
biological process
    GO:0002543    activation of blood coagulation via clotting cascade    Any process that initiates the clotting cascade of blood coagulation, a cascade of plasma enzymes that is triggered following damage to blood vessels, leading to formation of a clot.
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0002541    activation of plasma proteins involved in acute inflammatory response    Any process activating plasma proteins by proteolysis as part of an acute inflammatory response.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    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:0007598    blood coagulation, extrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the self-limited process linking exposure and activation of tissue factor to the activation of clotting factor X.
    GO:0070301    cellular response to hydrogen peroxide    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 hydrogen peroxide (H2O2) stimulus.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0010641    positive regulation of platelet-derived growth factor receptor signaling pathway    Any process that increases the frequency, rate or extent of the platelet-derived growth factor receptor signaling pathway.
    GO:0050927    positive regulation of positive chemotaxis    Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0014911    positive regulation of smooth muscle cell migration    Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration.
    GO:0032355    response to estradiol    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0034405    response to fluid shear stress    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 fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0055098    response to low-density lipoprotein particle stimulus    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 low-density lipoprotein particle stimulus.
    GO:0009612    response to mechanical stimulus    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 mechanical stimulus.
    GO:0009266    response to temperature stimulus    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 temperature 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.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    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:0031233    intrinsic component of external side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that penetrate the external side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        TF_HUMAN | P137261ahw 1boy 1dan 1fak 1j9c 1jps 1nl8 1o5d 1tfh 1w0y 1w2k 1wqv 1wss 1wtg 1wun 1wv7 1z6j 2a2q 2aei 2aer 2b7d 2b8o 2c4f 2cef 2ceh 2cez 2cfj 2ec9 2f9b 2fir 2flb 2flr 2hft 2puq 2zp0 2zwl 2zzu 3ela 3th2 3th3 3th4 4ibl 4m7l 4ylq 4z6a 4zma 5w06

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1UJ3)