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(-) Description

Title :  SOLUTION STRUCTURE OF THE STN_TRAF3IP1_ND DOMAIN OF INTERLEUKIN 13 RECEPTOR ALPHA 1-BINDING PROTEIN-1 [HOMO SAPIENS]
 
Authors :  W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Stn_traf3Ip1_nd Domain, Interleukin 13 Receptor Alpha 1-Binding Protein-1 [Homo Sapiens], Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of The Stn_traf3Ip1_nd Domain Of Interleukin 13 Receptor Alpha 1-Binding Protein-1 [Homo Sapiens]
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TNF RECEPTOR-ASSOCIATED FACTOR 3-INTERACTING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression System PlasmidP060925-07
    Expression System Vector TypePLASMID
    FragmentSTN_TRAF3IP1_ND DOMAIN, UNP RESIDUES 1-133
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymINTERLEUKIN 13 RECEPTOR ALPHA 1-BINDING PROTEIN 1, MIP-T3

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2EQO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Arg A:26 -Pro A:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

NMR Structure (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075068I17SMIPT3_HUMANDisease (SLSN9)  ---AI24S
2UniProtVAR_075069V125AMIPT3_HUMANDisease (SLSN9)  ---AV132A
3UniProtVAR_075070V125MMIPT3_HUMANDisease (SLSN9)  ---AV132M

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EQO)

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003733271aENSE00001904797chr2:239229082-239229426345MIPT3_HUMAN1-41411A:8-4841
1.2ENST000003733272ENSE00001627179chr2:239233947-23923401569MIPT3_HUMAN42-64231A:49-7123
1.3ENST000003733273ENSE00001677893chr2:239234450-239234611162MIPT3_HUMAN65-118541A:72-12554
1.4ENST000003733274ENSE00001750617chr2:239237327-239237470144MIPT3_HUMAN119-166481A:126-14015
1.5ENST000003733275ENSE00001618616chr2:239237567-239237983417MIPT3_HUMAN167-3051390--
1.6ENST000003733276ENSE00001460256chr2:239241465-23924153672MIPT3_HUMAN306-329240--
1.7ENST000003733277ENSE00001460255chr2:239242601-23924267676MIPT3_HUMAN330-355260--
1.8ENST000003733278ENSE00001460253chr2:239247003-23924709896MIPT3_HUMAN355-387330--
1.9aENST000003733279aENSE00001460252chr2:239253138-239253239102MIPT3_HUMAN387-421350--
1.11bENST0000037332711bENSE00001460251chr2:239256096-23925611621MIPT3_HUMAN421-42880--
1.12ENST0000037332712ENSE00001460249chr2:239257405-23925748985MIPT3_HUMAN428-456290--
1.13ENST0000037332713ENSE00001460248chr2:239257966-23925804984MIPT3_HUMAN456-484290--
1.14ENST0000037332714ENSE00001460247chr2:239261468-239261591124MIPT3_HUMAN484-525420--
1.15ENST0000037332715ENSE00001460246chr2:239261814-23926185037MIPT3_HUMAN526-538130--
1.16ENST0000037332716ENSE00001460245chr2:239264645-23926472177MIPT3_HUMAN538-563260--
1.17bENST0000037332717bENSE00001460244chr2:239306100-239306320221MIPT3_HUMAN564-637740--
1.18dENST0000037332718dENSE00001956209chr2:239307395-2393095412147MIPT3_HUMAN637-691550--

(-) Sequences/Alignments

NMR Structure
   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:140
 aligned with MIPT3_HUMAN | Q8TDR0 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:140
                                   1                                                                                                                                    
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133
          MIPT3_HUMAN     - -------MNAAVVRRTQEALGKVIRRPPLTEKLLSKPPFRYLHDIITEVIRMTGFMKGLYTDAEMKSDNVKDKDAKISFLQKAIDVVVMVSGEPLLAKPARIVAGHEPERTNELLQIIGKCCLNKLSSDDAVRRVLAGEK 133
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh...............hhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhhhhhhhhh.......hhhh.....hhhhhhhhhhhhhhhh......hhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) -----------------------S-----------------------------------------------------------------------------------------------------------A-------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------M-------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 -------Exon 1.1a  PDB: A:8-48 UniProt: 1-41     Exon 1.2  PDB: A:49-71 Exon 1.3  PDB: A:72-125 UniProt: 65-118               Exon 1.4        Transcript 1
                 2eqo A   1 GSSGSSGMNAAVVRRTQEALGKVIRRPPLTEKLLSKPPFRYLHDIITEVIRMTGFMKGLYTDAEMKSDNVKDKDAKISFLQKAIDVVVMVSGEPLLAKPARIVAGHEPERTNELLQIIGKCCLNKLSSDDAVRRVLAGEK 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

   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 2EQO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EQO)

(-) Gene Ontology  (29, 29)

NMR Structure(hide GO term definitions)
Chain A   (MIPT3_HUMAN | Q8TDR0)
molecular function
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0031076    embryonic camera-type eye development    The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure.
    GO:0042733    embryonic digit morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe.
    GO:0035050    embryonic heart tube development    The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field.
    GO:0042073    intraciliary transport    The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0001738    morphogenesis of a polarized epithelium    The morphogenetic process in which the anatomical structures of a polarized epithelium are generated and organized. A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis.
    GO:0050687    negative regulation of defense response to virus    Any process that stops, prevents or reduces the rate or extent of antiviral mechanisms, thereby facilitating viral replication.
    GO:0032688    negative regulation of interferon-beta production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-beta production.
    GO:0031333    negative regulation of protein complex assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:1901621    negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning    Any process that stops, prevents or reduces the frequency, rate or extent of smoothened signaling pathway involved in dorsal/ventral neural tube patterning.
    GO:0032480    negative regulation of type I interferon production    Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0021532    neural tube patterning    The regionalization process that regulates the coordinated growth that establishes the non-random spatial arrangement of the neural tube.
    GO:0036342    post-anal tail morphogenesis    The process in which a post-anal tail is generated and organized. A post-anal tail is a muscular region of the body that extends posterior to the anus. The post-anal tail may aid locomotion and balance.
    GO:0070507    regulation of microtubule cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
cellular component
    GO:0005930    axoneme    The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0036064    ciliary basal body    A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport.
    GO:0097546    ciliary base    Area of the cilium (also called flagellum) where the basal body and the axoneme are anchored to the plasma membrane. The ciliary base encompasses the distal part of the basal body, transition fibers and transition zone and is structurally and functionally very distinct from the rest of the cilium. In this area proteins are sorted and filtered before entering the cilium, and many ciliary proteins localize specifically to this area.
    GO:0097542    ciliary tip    Part of the cilium where the axoneme ends. The ciliary tip has been implicated in ciliary assembly and disassembly, as well as signal transduction.
    GO:0035869    ciliary transition zone    A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0030992    intraciliary transport particle B    The larger subcomplex of the intraciliary transport particle; characterized complexes have molecular weights around 550 kDa.

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    Arg A:26 - Pro A:27   [ RasMol ]  
 

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