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(-) Description

Title :  X-RAY STRUCTURE OF HUMAN PP25 GENE PRODUCT, HSPC034. NORTHEAST STRUCTURAL GENOMICS TARGET HR1958.
 
Authors :  A. P. Kuzin, S. M. Vorobiev, I. Lee, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  29 Jun 04  (Deposition) - 09 Nov 04  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Cell Cycle, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. A. Ramelot, S. Raman, A. P. Kuzin, R. Xiao, L. C. Ma, T. B. Acton, J. F. Hunt, G. T. Montelione, D. Baker, M. A. Kennedy
Improving Nmr Protein Structure Quality By Rosetta Refinement: A Molecular Replacement Study.
Proteins V. 75 147 2009
PubMed-ID: 18816799  |  Reference-DOI: 10.1002/PROT.22229
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LOC51668 PROTEIN
    ChainsA
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHIS PROTEIN IS PROBABLY A MUTANT BECAUSE ASP109 IS DELETED.
    SynonymANAPHASE-PROMOTING COMPLEX, SUBUNIT 10 (APC10), HR1958

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2SM1Ligand/IonSAMARIUM (III) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:29 , ASP A:32 , ASN A:34 , THR A:37 , HIS A:130 , HOH A:334BINDING SITE FOR RESIDUE CA A 221
2AC2SOFTWAREASP A:92BINDING SITE FOR RESIDUE SM A 331

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:45 -Pro A:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000001942142aENSE00001841796chr1:54411602-54411228375IFT25_HUMAN-00--
1.3bENST000001942143bENSE00001334213chr1:54405770-54405658113IFT25_HUMAN1-33331A:4-3330
1.4aENST000001942144aENSE00000772733chr1:54395818-54395712107IFT25_HUMAN33-69371A:33-6937
1.5bENST000001942145bENSE00001242678chr1:54394113-5439404569IFT25_HUMAN69-92241A:69-9224
1.6aENST000001942146aENSE00001242673chr1:54389620-5438957744IFT25_HUMAN92-106151A:92-10615
1.7cENST000001942147cENSE00001455098chr1:54387440-54387234207IFT25_HUMAN107-144381A:107-140 (gaps)34

(-) 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:136
 aligned with IFT25_HUMAN | Q9Y547 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:137
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       
          IFT25_HUMAN     4 IDLCLSSEGSEVILATSSDEKHPPENIIDGNPETFWTTTGMFPQEFIICFHKHVRIERLVIQSYFVQTLKIEKSTSKEPVDFEQWIEKDLVHTEGQLQNEEIVAHDGSATYLRFIIVSAFDHFASVHSVSAEGTVVS 140
               SCOP domains d1tvga_ A: Placental protein 25, pp25                                                                                                     SCOP domains
               CATH domains 1tvgA00 A:4-140 Galactose-binding domain-like                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.eee.........hhhhhhh......ee......eeeeeeeeeeeeeeeeeeeee.eeeeeeeee........eeeeeee........eeeee...-eeeeeeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:4-33        -----------------------------------Exon 1.5b  PDB: A:69-92 --------------Exon 1.7c  PDB: A:107-140 (gaps)   Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.4a  PDB: A:33-69              ----------------------Exon 1.6a      ---------------------------------- Transcript 1 (2)
                 1tvg A   4 IDLCLSSEGSEVILATSSDEKHPPENIIDGNPETFWTTTGMFPQEFIICFHKHVRIERLVIQSYFVQTLKIEKSTSKEPVDFEQWIEKDLVHTEGQLQNEEIVAH-GSATYLRFIIVSAFDHFASVHSVSAEGTVVS 140
                                    13        23        33        43        53        63        73        83        93       103    | |113       123       133       
                                                                                                                                  108 |                              
                                                                                                                                    110                              

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IFT25_HUMAN | Q9Y547)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0070986    left/right axis specification    The establishment, maintenance and elaboration of the left/right axis. The left/right axis is defined by a line that runs orthogonal to both the anterior/posterior and dorsal/ventral axes. Each side is defined from the viewpoint of the organism rather of the observer (as per anatomical axes).
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0007224    smoothened signaling pathway    A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    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: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: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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        IFT25_HUMAN | Q9Y5471xpw

(-) Related Entries Specified in the PDB File

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