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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-008, FN3 DOMAIN IN HUMAN CDNA
 
Authors :  Y. Doi-Katayama, F. Hayashi, H. Hirota, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Nov 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Fn3 Domain, Human Cdna, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Doi-Katayama, F. Hayashi, H. Hirota, S. Yokoyama
Solution Structure Of Rsgi Ruh-008, A Fn3 Domain In Human Cdna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIAA1355 PROTEIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP021007-47
    Expression System Vector TypePLASMID
    FragmentFN3 DOMAIN
    GeneKAZUSA CDNA KIAA1355
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymRSGI RUH-008

 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 1V5J)

(-) Sites  (0, 0)

(no "Site" information available for 1V5J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V5J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V5J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V5J)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.TUTLA_HUMAN507-611
623-718
  1-
A:8-102

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003680941bENSE00001329537chr1:159915386-15991536324TUTLA_HUMAN-00--
1.2ENST000003680942ENSE00002175139chr1:159913418-159913187232TUTLA_HUMAN1-20200--
1.3ENST000003680943ENSE00000904974chr1:159912941-159912753189TUTLA_HUMAN20-83640--
1.4ENST000003680944ENSE00000904973chr1:159907628-159907476153TUTLA_HUMAN83-134520--
1.5ENST000003680945ENSE00000904972chr1:159906698-159906544155TUTLA_HUMAN134-185520--
1.6ENST000003680946ENSE00000904971chr1:159906306-159906189118TUTLA_HUMAN186-225400--
1.7ENST000003680947ENSE00000904970chr1:159904612-159904471142TUTLA_HUMAN225-272480--
1.8ENST000003680948ENSE00000904969chr1:159904360-159904215146TUTLA_HUMAN272-321500--
1.9aENST000003680949aENSE00000904968chr1:159904122-159903980143TUTLA_HUMAN321-368480--
1.10bENST0000036809410bENSE00000904967chr1:159902442-159902302141TUTLA_HUMAN369-415470--
1.11cENST0000036809411cENSE00000904966chr1:159901718-159901602117TUTLA_HUMAN416-454390--
1.11dENST0000036809411dENSE00000904965chr1:159901393-159901243151TUTLA_HUMAN455-505510--
1.12ENST0000036809412ENSE00000904964chr1:159901051-159900928124TUTLA_HUMAN505-546420--
1.13ENST0000036809413ENSE00001231012chr1:159900657-159900482176TUTLA_HUMAN546-605601A:1-7 (gaps)15
1.14aENST0000036809414aENSE00001231002chr1:159900229-159899979251TUTLA_HUMAN605-688841A:7-72 (gaps)84
1.14cENST0000036809414cENSE00001067998chr1:159899765-15989968185TUTLA_HUMAN689-717291A:73-10129
1.15aENST0000036809415aENSE00001230986chr1:159899604-159899428177TUTLA_HUMAN717-776601A:101-108 (gaps)22
1.16aENST0000036809416aENSE00001231083chr1:159899183-15989914143TUTLA_HUMAN776-790150--
1.16cENST0000036809416cENSE00001067981chr1:159898808-159897948861TUTLA_HUMAN790-10772880--
1.17ENST0000036809417ENSE00001040401chr1:159897677-159897550128TUTLA_HUMAN1077-1120440--
1.18bENST0000036809418bENSE00001231076chr1:159897316-159896829488TUTLA_HUMAN1120-1179600--

(-) 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:108
 aligned with TUTLA_HUMAN | Q9P2J2 from UniProtKB/Swiss-Prot  Length:1179

    Alignment length:148
                                   600       610       620       630       640       650       660       670       680       690       700       710       720       730        
          TUTLA_HUMAN   591 GSGPFSEIVLSAPEGLPTTPAAPGLPPTEIPPPLSPPRGLVAVRTPRGVLLHWDPPELVPKRLDGYVLEGRQGSQGWEVLDPAVAGTETELLVPGLIKDVLYEFRLVAFAGSFVSDPSNTANVSTSGLEVYPSRTQLPGLLPQPVLAG 738
               SCOP domains d1        v5ja_                   A: KIAA1355                                                                                                        SCOP domains
               CATH domains 1v        5jA00                   A:1-108 Immunoglobulins                                                                                            CATH domains
               Pfam domains ----------------------------------fn3-1v5jA01 A:9-92                                                                  ------------------------------ Pfam domains
         Sec.struct. author ..--------.....------------------....eeeeeeee..eeeeeee...........eeeeeee.....eeeeeee.....eeee...................eeeeeeeeee........-..-------------.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FN3  PDB: -          -----------FN3  PDB: A:8-102 UniProt: 623-718                                                              -------------------- PROSITE
           Transcript 1 (1) Exon 1.13      -----------------------------------------------------------------------------------Exon 1.14c  PDB: A:73-101    --------------------- Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.14a  PDB: A:7-72 (gaps) UniProt: 605-688                                     ----------------------------Exon 1.15a             Transcript 1 (2)
                 1v5j A   1 GS--------SGSSG------------------LSPPRGLVAVRTPRGVLLHWDPPELVPKRLDGYVLEGRQGSQGWEVLDPAVAGTETELLVPGLIKDVLYEFRLVAFAGSFVSDPSNTANVSTSGLSG-PS-------------SG 108
                             |       -|   |    -         -   |    14        24        34        44        54        64        74        84        94       104 ||      -      | 
                             2        3   7                  8                                                                                             104 ||           107 
                                                                                                                                                             105|               
                                                                                                                                                              106               

   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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: E-set (290)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (TUTLA_HUMAN | Q9P2J2)
molecular function
    GO:0098632    protein binding involved in cell-cell adhesion    Any protein binding that is involved in cell-cell adhesion.
biological process
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0016358    dendrite development    The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0007156    homophilic cell adhesion via plasma membrane adhesion molecules    The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0050807    regulation of synapse organization    Any process that modulates the physical form of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0060077    inhibitory synapse    A synapse in which an action potential in the presynaptic cell reduces the probability of an action potential occurring in the postsynaptic cell.
    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.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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