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(-) Description

Title :  CRYSTAL STRUCTURE OF IIGP1: A PARADIGM FOR INTERFERON INDUCIBLE P47 RESISTANCE GTPASES
 
Authors :  A. Ghosh, R. Uthaiah, J. Howard, C. Herrmann, E. Wolf
Date :  16 Jun 04  (Deposition) - 21 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Gtpase, Interferon Gamma, Crystal Structure, Dimer, Immunology, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Ghosh, R. Uthaiah, J. Howard, C. Herrmann, E. Wolf
Crystal Structure Of Iigp1; A Paradigm For Interferon-Inducible P47 Resistance Gtpases
Mol. Cell V. 15 727 2004
PubMed-ID: 15350217  |  Reference-DOI: 10.1016/J.MOLCEL.2004.07.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERFERON-INDUCIBLE GTPASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX4T1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneIIGP1
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymIIGP1

 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
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:83 , LYS A:101 , ASP A:126 , GNP A:500BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREGLU A:77 , THR A:78 , GLY A:79 , SER A:80 , GLY A:81 , LYS A:82 , SER A:83 , SER A:84 , THR A:102 , GLY A:103 , GLU A:106 , LYS A:184 , ASP A:186 , SER A:231 , ASN A:232 , LYS A:233 , MG A:501BINDING SITE FOR RESIDUE GNP A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TQ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TQ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TQ6)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_IRGPS51716 IRG-type guanine nucleotide-binding (G) domain profile.IIGP1_MOUSE68-250  1A:68-250

(-) Exons   (0, 0)

(no "Exon" information available for 1TQ6)

(-) 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:402
 aligned with IIGP1_MOUSE | Q9QZ85 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:402
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411  
          IIGP1_MOUSE    12 ENNDLPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPNTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISMMKKEFYFVRTKVDSDITNEADGKPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVSLPNITDSVIEKKRQFLKQRIWLEGFAADLVNIIPSLTFLLDSDLETLKKSMKFYRTVFGVDETSLQRLARDWEIEVDQVEAMIKSPAVFKPTDEETIQERLSRYIQEFCLANGYLLPKNSFLKEIFYLKYYFLDMVTEDAKTLLKEICLRN 413
               SCOP domains d1tq6a_ A: Interferon-inducible GTPase                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------IIGP-1tq6A01 A:35-409                                                                                                                                                                                                                                                                                                                                                                  ---- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhh.............hhhhhhh..eeee......eeeee..hhhhh..hhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......eee.........hhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhh..............hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------G_IRG  PDB: A:68-250 UniProt: 68-250                                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tq6 A  12 ENNDLPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISAMKKEFYFVRTKVDSDITNEADGEPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVSLPNITDSVIEKKRQFLKQRIWLEGFAADLVNIIPSLTFLLDSDLETLKKSMKFYRTVFGVDETSLQRLARDWEIEVDQVEAMIKSPAVFKPTDEETIQERLSRYIQEFCLANGYLLPKNSFLKEIFYLKYYFLDMVTEDAKTLLKEICLRN 413
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411  

   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "CATH Domain" information available for 1TQ6)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IIGP1_MOUSE | Q9QZ85)
molecular function
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0035458    cellular response to interferon-beta    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-beta stimulus. Interferon-beta is a type I interferon.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0042832    defense response to protozoan    Reactions triggered in response to the presence of a protozoan that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0032580    Golgi cisterna membrane    The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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.
    GO:0020005    symbiont-containing vacuole membrane    The lipid bilayer surrounding a symbiont-containing vacuole, derived from both the host and symbiont.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IIGP1_MOUSE | Q9QZ851tpz 1tq2 1tq4 1tqd 4lv5 4lv8 5fph

(-) Related Entries Specified in the PDB File

1dg3
1f5n
1tpz THE SAME PROTEIN WITH GDP
1tq2 THE SAME PROTEIN WITH GNP
1tq4 THE SAME PROTEIN, K48A MUTANT WITH GDP
1tqd THE SAME PROTEIN WITHOUT NUCLEOTIDE