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(-) Description

Title :  CRYSTAL STRUCTURE OF RABBIT GITRL
 
Authors :  P. R. Kumar, R. Bhosle, A. Gizzi, A. Scott Glenn, S. Chowhury, B. Hiller R. Seidel, S. G. Nathenson, S. C. Almo, New York Structural Genomic Research Consortium (Nysgrc), Atoms-To-Animals: The Immune F Network (Ifn)
Date :  13 Jan 12  (Deposition) - 21 Mar 12  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  A  (12x)
Keywords :  Gitrl, Glucocorticoid-Induced Tnf Receptor Ligand, Immune System, Tnfrsf18, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. R. Kumar, R. Bhosle, A. Gizzi, A. Scott Glenn, S. Chowhury, B. Hillerich, R. Seidel, S. G. Nathenson, S. C. Almo
Crystal Structure Of Gitrl From Oryctolagus Cuniculus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 18
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GITRL, TNFSF18
    Organism Common: EUROPEAN RABBIT,JAPANESE WHITE RABBIT,DOMESTIC RABBIT,RABBITS
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A
Biological Unit 2 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1B3P1Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1B3P3Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1B3P12Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:19 , GLU A:20 , PRO A:22 , ASN A:40 , ASP A:91 , GLN A:122 , PHE A:123 , SER A:125 , HOH A:331 , HOH A:365 , HOH A:391 , HOH A:421 , HOH A:422BINDING SITE FOR RESIDUE B3P A 201

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:6 -A:26

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:11 -Pro A:12
2Leu A:13 -Pro A:14
3Glu A:20 -Pro A:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DB5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DB5)

(-) Exons   (0, 0)

(no "Exon" information available for 4DB5)

(-) 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:121
 aligned with G1TIM1_RABIT | G1TIM1 from UniProtKB/TrEMBL  Length:189

    Alignment length:121
                                    78        88        98       108       118       128       138       148       158       168       178       188 
         G1TIM1_RABIT    69 ACVAKFGPLPSKWQMEPPKPSCVNKISDWKLKILQNGLYIIYGQVAPDPTYKGFAPFEVQLCKNKEAIQTLTNNSKIQNLGGIYEFDAGDIIELRFNSDDQVLKNNTYWGIVLLVTPQFSS 189
               SCOP domains d4db5a_ A: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeee......eeeee..eeee...eeeeeeeee.............eeeee..eeeeee......eeeeeeeee....eeeeee.hhhhhhhhhheeeeeeee.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4db5 A   5 ACVAKFGPLPSKWQMEPPKPSCVNKISDWKLKILQNGLYIIYGQVAPDPTYKGFAPFEVQLCKNKEAIQTLTNNSKIQNLGGIYEFDAGDIIELRFNSDDQVLKNNTYWGIVLLVTPQFSS 125
                                    14        24        34        44        54        64        74        84        94       104       114       124
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DB5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DB5)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (G1TIM1_RABIT | G1TIM1)
molecular function
    GO:0032813    tumor necrosis factor receptor superfamily binding    Interacting selectively and non-covalently with any member of the tumor necrosis factor receptor superfamily.
biological process
    GO:0002309    T cell proliferation involved in immune response    The expansion of a T cell population by cell division as part of an immune response.
    GO:2000329    negative regulation of T-helper 17 cell lineage commitment    Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 17 cell lineage commitment.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0002687    positive regulation of leukocyte migration    Any process that activates or increases the frequency, rate, or extent of leukocyte migration.
    GO:0010759    positive regulation of macrophage chemotaxis    Any process that increases the rate, frequency or extent of macrophage chemotaxis. Macrophage chemotaxis is the movement of a macrophage in response to an external stimulus.
    GO:0090026    positive regulation of monocyte chemotaxis    Any process that increases the frequency, rate, or extent of monocyte chemotaxis.
    GO:0090073    positive regulation of protein homodimerization activity    Any process that increases the frequency, rate or extent of protein homodimerization, interacting selectively with an identical protein to form a homodimer.
    GO:0042129    regulation of T cell proliferation    Any process that modulates the frequency, rate or extent of T cell proliferation.
    GO:2000508    regulation of dendritic cell chemotaxis    Any process that modulates the frequency, rate or extent of dendritic cell chemotaxis.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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.

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