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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TOB1 PROTEIN
 
Authors :  K. Saito, S. Kishishita, A. Nishino, K. Murayama, T. Terada, M. Shirouzu, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  08 May 07  (Deposition) - 13 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Human Tob1 Protein, Phosphorylation, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Saito, S. Kishishita, A. Nishino, K. Murayama, T. Terada, M. Shirouzu, T. Kigawa, S. Yokoyama
Crystal Structure Of Human Tob1 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN TOB1
    ChainsA, B, C, D
    EngineeredYES
    Expression System PlasmidPK051011-08
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-117
    GeneTOB1, TOB, TROB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymTRANSDUCER OF ERBB-2 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2Z15)

(-) Sites  (0, 0)

(no "Site" information available for 2Z15)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z15)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z15)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z15)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BTG_1PS00960 BTG family signature 1.TOB1_HUMAN40-60
 
 
 
  4A:49-69
B:49-69
C:49-69
D:49-69
2BTG_2PS01203 BTG family signature 2.TOB1_HUMAN86-105
 
 
 
  4A:95-114
B:95-114
C:95-114
D:95-114
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BTG_1PS00960 BTG family signature 1.TOB1_HUMAN40-60
 
 
 
  1A:49-69
-
-
-
2BTG_2PS01203 BTG family signature 2.TOB1_HUMAN86-105
 
 
 
  1A:95-114
-
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BTG_1PS00960 BTG family signature 1.TOB1_HUMAN40-60
 
 
 
  1-
B:49-69
-
-
2BTG_2PS01203 BTG family signature 2.TOB1_HUMAN86-105
 
 
 
  1-
B:95-114
-
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BTG_1PS00960 BTG family signature 1.TOB1_HUMAN40-60
 
 
 
  1-
-
C:49-69
-
2BTG_2PS01203 BTG family signature 2.TOB1_HUMAN86-105
 
 
 
  1-
-
C:95-114
-
Biological Unit 4 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BTG_1PS00960 BTG family signature 1.TOB1_HUMAN40-60
 
 
 
  1-
-
-
D:49-69
2BTG_2PS01203 BTG family signature 2.TOB1_HUMAN86-105
 
 
 
  1-
-
-
D:95-114

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002689571ENSE00001757872chr17:48945339-48945166174TOB1_HUMAN-00--
1.2ENST000002689572ENSE00001685727chr17:48944963-48944855109TOB1_HUMAN-00--
1.4aENST000002689574aENSE00000947126chr17:48941524-489403411184TOB1_HUMAN1-3943944A:10-126
B:10-125
C:10-125
D:10-125
117
116
116
116

(-) 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:119
 aligned with TOB1_HUMAN | P50616 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:119
                              1                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108         
           TOB1_HUMAN     - --MQLEIQVALNFIISYLYNKLPRRRVNIFGEELERLLKKKYEGHWYPEKPYKGSGFRCIHIGEKVDPVIEQASKESGLDIDDVRGNLPQDLSVWIDPFEVSYQIGEKGPVKVLYVDDN 117
               SCOP domains --d2z15a1 A:10-126 TOB1, N-terminal domain                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..........hhhhhheee....hhhhhhhhhh...hhhhhhhhh...eeeeee..eeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------BTG_1  PDB: A:49-69  -------------------------BTG_2  PDB: A:95-114------------ PROSITE
               Transcript 1 --Exon 1.4a  PDB: A:10-126 UniProt: 1-394 [INCOMPLETE]                                                                  Transcript 1
                 2z15 A   8 SGMQLEIQVALNFIISYLYNKLPRRRVNIFGEELERLLKKKYEGHWYPEKPYKGSGFRCIHIGEKVDPVIEQASKESGLDIDDVRGNLPQDLSVWIDPFEVSYQIGEKGPVKVLYVDDN 126
                                    17        27        37        47        57        67        77        87        97       107       117         

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with TOB1_HUMAN | P50616 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:120
                                1                                                                                                                   
                                |    6        16        26        36        46        56        66        76        86        96       106       116
           TOB1_HUMAN     - ----MQLEIQVALNFIISYLYNKLPRRRVNIFGEELERLLKKKYEGHWYPEKPYKGSGFRCIHIGEKVDPVIEQASKESGLDIDDVRGNLPQDLSVWIDPFEVSYQIGEKGPVKVLYVDD 116
               SCOP domains d2z15b_ B: TOB1, N-terminal domain                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..........hhhhhheee....hhhhhhhhhhhh.hhhhhhhhh...eeeeee..eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------BTG_1  PDB: B:49-69  -------------------------BTG_2  PDB: B:95-114----------- PROSITE
               Transcript 1 ----Exon 1.4a  PDB: B:10-125 UniProt: 1-394 [INCOMPLETE]                                                                 Transcript 1
                 2z15 B   6 GSSGMQLEIQVALNFIISYLYNKLPRRRVNIFGEELERLLKKKYEGHWYPEKPYKGSGFRCIHIGEKVDPVIEQASKESGLDIDDVRGNLPQDLSVWIDPFEVSYQIGEKGPVKVLYVDD 125
                                    15        25        35        45        55        65        75        85        95       105       115       125

Chain C from PDB  Type:PROTEIN  Length:117
 aligned with TOB1_HUMAN | P50616 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:117
                             1                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       
           TOB1_HUMAN     - -MQLEIQVALNFIISYLYNKLPRRRVNIFGEELERLLKKKYEGHWYPEKPYKGSGFRCIHIGEKVDPVIEQASKESGLDIDDVRGNLPQDLSVWIDPFEVSYQIGEKGPVKVLYVDD 116
               SCOP domains d2z15c_ C: TOB1, N-terminal domain                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..........hhhhhheee....hhhhhhhhhhh..hhhhhhh.....eeeeee..eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------BTG_1  PDB: C:49-69  -------------------------BTG_2  PDB: C:95-114----------- PROSITE
               Transcript 1 -Exon 1.4a  PDB: C:10-125 UniProt: 1-394 [INCOMPLETE]                                                                 Transcript 1
                 2z15 C   9 GMQLEIQVALNFIISYLYNKLPRRRVNIFGEELERLLKKKYEGHWYPEKPYKGSGFRCIHIGEKVDPVIEQASKESGLDIDDVRGNLPQDLSVWIDPFEVSYQIGEKGPVKVLYVDD 125
                                    18        28        38        48        58        68        78        88        98       108       118       

Chain D from PDB  Type:PROTEIN  Length:120
 aligned with TOB1_HUMAN | P50616 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:120
                                1                                                                                                                   
                                |    6        16        26        36        46        56        66        76        86        96       106       116
           TOB1_HUMAN     - ----MQLEIQVALNFIISYLYNKLPRRRVNIFGEELERLLKKKYEGHWYPEKPYKGSGFRCIHIGEKVDPVIEQASKESGLDIDDVRGNLPQDLSVWIDPFEVSYQIGEKGPVKVLYVDD 116
               SCOP domains d2z15d_ D: TOB1, N-terminal domain                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----BTG-2z15D01 D:10-124                                                                                               - Pfam domains (1)
           Pfam domains (2) ----BTG-2z15D02 D:10-124                                                                                               - Pfam domains (2)
           Pfam domains (3) ----BTG-2z15D03 D:10-124                                                                                               - Pfam domains (3)
           Pfam domains (4) ----BTG-2z15D04 D:10-124                                                                                               - Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..........hhhhhheee....hhhhhhhhhhhh.hhhhhhhhh...eeeeee..eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------BTG_1  PDB: D:49-69  -------------------------BTG_2  PDB: D:95-114----------- PROSITE
               Transcript 1 ----Exon 1.4a  PDB: D:10-125 UniProt: 1-394 [INCOMPLETE]                                                                 Transcript 1
                 2z15 D   6 GSSGMQLEIQVALNFIISYLYNKLPRRRVNIFGEELERLLKKKYEGHWYPEKPYKGSGFRCIHIGEKVDPVIEQASKESGLDIDDVRGNLPQDLSVWIDPFEVSYQIGEKGPVKVLYVDD 125
                                    15        25        35        45        55        65        75        85        95       105       115       125

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z15)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Family: BTG (1)
1aBTG-2z15D01D:10-124
1bBTG-2z15D02D:10-124
1cBTG-2z15D03D:10-124
1dBTG-2z15D04D:10-124

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TOB1_HUMAN | P50616)
molecular function
    GO:0005070    SH3/SH2 adaptor activity    Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
    GO:0046332    SMAD binding    Interacting selectively and non-covalently with a SMAD signaling protein.
    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:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
biological process
    GO:0007184    SMAD protein import into nucleus    The directed movement of a SMAD proteins from the cytoplasm into the nucleus. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0030514    negative regulation of BMP signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0060212    negative regulation of nuclear-transcribed mRNA poly(A) tail shortening    Any process that decreases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length.
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0045668    negative regulation of osteoblast differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:1900153    positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.
    GO:0060213    positive regulation of nuclear-transcribed mRNA poly(A) tail shortening    Any process that increases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
cellular component
    GO:0030014    CCR4-NOT complex    The evolutionarily conserved CCR4-NOT complex is involved in several aspects of mRNA metabolism, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. In Saccharomyces the CCR4-NOT complex comprises a core complex of 9 proteins (Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p), Caf4p, Caf16p, and several less well characterized proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

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        TOB1_HUMAN | P506162d5r 5ci8 5ci9

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