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(-) Description

Title :  HUMAN THROMBOPOIETIN FUNCTIONAL DOMAIN COMPLEXED TO NEUTRALIZING ANTIBODY TN1 FAB
 
Authors :  M. D. Feese, T. Tamada, Y. Kato, Y. Maeda, M. Hirose, Y. Matsukura, H. Shigematsu, T. Kato, H. Miyazaki, R. Kuroki
Date :  18 Dec 03  (Deposition) - 02 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym. Unit :  H,I,L,M,V,X
Biol. Unit 1:  H,L,V  (1x)
Biol. Unit 2:  I,M,X  (1x)
Keywords :  Thrombopoietin, Fab Fragment, Complex (Cytokine/Antibody), Immune System/Cytokine Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. D. Feese, T. Tamada, Y. Kato, Y. Maeda, M. Hirose, Y. Matsukura, H. Shigematsu, T. Muto, A. Matsumoto, H. Watarai, K. Ogami, T. Tahara, T. Kato, H. Miyazaki, R. Kuroki
Structure Of The Receptor-Binding Domain Of Human Thrombopoietin Determined By Complexation With A Neutralizing Antibody Fragment
Proc. Natl. Acad. Sci. Usa V. 101 1816 2004
PubMed-ID: 14769915  |  Reference-DOI: 10.1073/PNAS.0308530100
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MONOCLONAL TN1 FAB LIGHT CHAIN
    ChainsL, M
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Cell LineHYBRIDOMA
    Expression System CommonHOUSE MOUSE
    Expression System Taxid10090
    FragmentFAB LIGHT CHAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - MONOCLONAL TN1 FAB HEAVY CHAIN
    ChainsH, I
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Cell LineHYBRIDOMA
    Expression System CommonHOUSE MOUSE
    Expression System Taxid10090
    FragmentFAB HEAVY CHAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - THROMBOPOIETIN
    ChainsV, X
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentTPO FUNCTIONAL DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMEGAKARYOCYTE COLONY STIMULATING FACTOR, MYELOPROLIFERATIVE LEUKEMIA VIRUS ONCOGENE LIGAND, C-MPL LIGAND, ML, MEGAKARYOCYTE GROWTH AND DEVELOPMENT FACTOR, MGDF

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit HILMVX
Biological Unit 1 (1x)H L V 
Biological Unit 2 (1x) I M X

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1V7M)

(-) Sites  (0, 0)

(no "Site" information available for 1V7M)

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1H:22 -H:98
2H:143 -H:198
3I:22 -I:98
4I:143 -I:198
5L:23 -L:87
6L:133 -L:193
7M:23 -M:87
8M:133 -M:193
9V:7 -V:151
10V:29 -V:85
11X:7 -X:151
12X:29 -X:85

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Tyr L:93 -Pro L:94
2Tyr L:139 -Pro L:140
3Phe H:149 -Pro H:150
4Glu H:151 -Pro H:152
5Trp H:191 -Pro H:192
6Tyr M:93 -Pro M:94
7Tyr M:139 -Pro M:140
8Phe I:149 -Pro I:150
9Glu I:151 -Pro I:152
10Trp I:191 -Pro I:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011796G116ETPO_HUMANPolymorphism1126665V/XG95E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011796G116ETPO_HUMANPolymorphism1126665VG95E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011796G116ETPO_HUMANPolymorphism1126665XG95E

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V7M)

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002046151aENSE00001288997chr3:184095932-18409586370TPO_HUMAN-00--
1.2aENST000002046152aENSE00001056827chr3:184094192-184094035158TPO_HUMAN1-550--
1.3ENST000002046153ENSE00001079331chr3:184093803-184093676128TPO_HUMAN5-47432V:7-26
X:7-26
20
20
1.4ENST000002046154ENSE00000781177chr3:184093389-18409330387TPO_HUMAN48-76292V:27-55
X:27-55
29
29
1.5aENST000002046155aENSE00000781178chr3:184091370-184091203168TPO_HUMAN77-132562V:56-111
X:56-111
56
56
1.6cENST000002046156cENSE00001288988chr3:184090966-1840897231244TPO_HUMAN133-3532212V:112-151
X:112-151
40
40

(-) 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 H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1v7mh1 H:1-116 Immunoglobulin heavy chain variable domain, VH                                                      d1v7mh2 H:117-217 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1v7mH01 H:1-116 Immunoglobulins                                                                                     1v7mH02 H:117-205 Immunoglobulins                                                        ------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee....eeeeeeeee..hhhhh.eeeeeee...eeeeeeee........eee.hhhh..eeeeee....eeeeeee..hhhhheeeeeee....ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhh....eeeeeee...eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v7m H   1 EVKLEESGGGLVQPGGSMKLSCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRSKVNNHAIHYAESVKGRFTVSRDDSKSSVYLQMNSLRAEDTGIYYCSGWSFLYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       

Chain I from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1v7mi1 I:1-116 Immunoglobulin heavy chain variable domain, VH                                                      d1v7mi2 I:117-217 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1v7mI01 I:1-116 Immunoglobulins                                                                                     1v7mI02 I:117-205 Immunoglobulins                                                        ------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee.hhhhh..eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee....ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v7m I   1 EVKLEESGGGLVQPGGSMKLSCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRSKVNNHAIHYAESVKGRFTVSRDDSKSSVYLQMNSLRAEDTGIYYCSGWSFLYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d1v7ml1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1v7ml2 L:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1v7mL01 L:1-107 Immunoglobulins                                                                            1v7mL02 L:108-209 Immunoglobulins                                                                     --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeeeeeee...eeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v7m L   1 QVVLTQSPGIMSASPGEKVTITCSASSSVSYMYWFQQKPGTSPKLWIYSTSNLASGVPARFRGSGSGTSYSLTISRMEAEDAATYYCQQRSGYPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  

Chain M from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d1v7mm1 M:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1v7mm2 M:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1v7mM01 M:1-107 Immunoglobulins                                                                            1v7mM02 M:108-209 Immunoglobulins                                                                     --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh...eeeeeee..eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v7m M   1 QVVLTQSPGIMSASPGEKVTITCSASSSVSYMYWFQQKPGTSPKLWIYSTSNLASGVPARFRGSGSGTSYSLTISRMEAEDAATYYCQQRSGYPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  

Chain V from PDB  Type:PROTEIN  Length:145
 aligned with TPO_HUMAN | P40225 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:145
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167     
            TPO_HUMAN    28 CDLRVLSKLLRDSHVLHSRLSQCPEVHPLPTPVLLPAVDFSLGEWKTQMEETKAQDILGAVTLLLEGVMAARGQLGPTCLSSLLGQLSGQVRLLLGALQSLLGTQLPPQGRTTAHKDPNAIFLSFQHLLRGKVRFLMLVGGSTLC 172
               SCOP domains d1v7mv_ V: Thrombopoietin                                                                                                                         SCOP domains
               CATH domains 1v7mV00 V:7-151  [code=1.20.1250.10, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh..........eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh........eeee.hhhhhhhhhhhhhhh.hhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------E-------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: V:7-2Exon 1.4  PDB: V:27-55       Exon 1.5a  PDB: V:56-111 UniProt: 77-132                Exon 1.6c  PDB: V:112-151 [INCOMPLETE]   Transcript 1
                 1v7m V   7 CDLRVLSKLLRDSHVLHSRLSQCPEVHPLPTPVLLPAVDFSLGEWKTQMEETKAQDILGAVTLLLEGVMAARGQLGPTCLSSLLGQLSGQVRLLLGALQSLLGTQLPPQGRTTAHKDPNAIFLSFQHLLRGKVRFLMLVGGSTLC 151
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146     

Chain X from PDB  Type:PROTEIN  Length:145
 aligned with TPO_HUMAN | P40225 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:145
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167     
            TPO_HUMAN    28 CDLRVLSKLLRDSHVLHSRLSQCPEVHPLPTPVLLPAVDFSLGEWKTQMEETKAQDILGAVTLLLEGVMAARGQLGPTCLSSLLGQLSGQVRLLLGALQSLLGTQLPPQGRTTAHKDPNAIFLSFQHLLRGKVRFLMLVGGSTLC 172
               SCOP domains d1v7mx_ X: Thrombopoietin                                                                                                                         SCOP domains
               CATH domains 1v7mX00 X:7-151  [code=1.20.1250.10, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.............eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------E-------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: X:7-2Exon 1.4  PDB: X:27-55       Exon 1.5a  PDB: X:56-111 UniProt: 77-132                Exon 1.6c  PDB: X:112-151 [INCOMPLETE]   Transcript 1
                 1v7m X   7 CDLRVLSKLLRDSHVLHSRLSQCPEVHPLPTPVLLPAVDFSLGEWKTQMEETKAQDILGAVTLLLEGVMAARGQLGPTCLSSLLGQLSGQVRLLLGALQSLLGTQLPPQGRTTAHKDPNAIFLSFQHLLRGKVRFLMLVGGSTLC 151
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146     

   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, 10)

Asymmetric Unit

(-) CATH Domains  (2, 10)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
2a1v7mL02L:108-209
2b1v7mH02H:117-205
2c1v7mI02I:117-205
2d1v7mH01H:1-116
2e1v7mI01I:1-116
2f1v7mM02M:108-209
2g1v7mL01L:1-107
2h1v7mM01M:1-107

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V7M)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain V,X   (TPO_HUMAN | P40225)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0005179    hormone activity    The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
biological process
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0030099    myeloid cell differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:1902035    positive regulation of hematopoietic stem cell proliferation    Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell proliferation.
    GO:0045654    positive regulation of megakaryocyte differentiation    Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation.
    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: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:0038163    thrombopoietin-mediated signaling pathway    A series of molecular signals initiated by the binding of a thrombopoietin to the thrombopoietin receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    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.

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    Glu H:151 - Pro H:152   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        TPO_HUMAN | P402251v7n

(-) Related Entries Specified in the PDB File

1v7n THE SAME PROTEIN(Q115R)