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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE ZB DOMAIN FROM THE RNA EDITING ENZYME ADAR1
 
Authors :  A. Athanasiadis, D. Placido, S. Maas, B. A. Brown Ii, K. Lowenhaupt, A. Rich
Date :  03 Oct 04  (Deposition) - 02 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.97
Chains :  Asym./Biol. Unit :  A
Keywords :  Winged Helix-Turn-Helix, Rna Editing, Interferon, Adar1, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Athanasiadis, D. Placido, S. Maas, B. A. Brown Ii, K. Lowenhaupt, A. Rich
The Crystal Structure Of The Z[Beta] Domain Of The Rna-Editing Enzyme Adar1 Reveals Distinct Conserved Surfaces Among Z-Domains.
J. Mol. Biol. V. 351 496 2005
PubMed-ID: 16023667  |  Reference-DOI: 10.1016/J.JMB.2005.06.028
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DOUBLE-STRANDED RNA-SPECIFIC ADENOSINE DEAMINASE
    ChainsA
    EC Number3.5.4.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneADAR, ADAR1, DSRAD, IFI4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDRADA, 136 KDA DOUBLE-STRANDED RNA BINDING PROTEIN, P136, K88DSRBP, INTERFERON-INDUCIBLE PROTEIN 4, IFI-4 PROTEIN, ADAR1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
2CL2Ligand/IonCHLORIDE ION
3NI1Ligand/IonNICKEL (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:304 , ASP A:312 , LYS A:359 , CD A:397 , CL A:399BINDING SITE FOR RESIDUE CD A 396
2AC2SOFTWAREGLU A:301 , CYS A:304 , ASP A:312 , ARG A:328 , HIS A:354 , CD A:396 , CL A:400BINDING SITE FOR RESIDUE CD A 397
3AC3SOFTWAREGLY A:288 , SER A:289 , HIS A:290BINDING SITE FOR RESIDUE NI A 398
4AC4SOFTWARELYS A:300 , CYS A:304 , ASP A:312 , LYS A:359 , CD A:396BINDING SITE FOR RESIDUE CL A 399
5AC5SOFTWAREARG A:328 , HIS A:354 , CD A:397BINDING SITE FOR RESIDUE CL A 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:349 -Pro A:350

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DRADA_REPEATPS50139 DRADA repeat profile.DSRAD_HUMAN133-202
293-360
  1-
A:294-360

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENST000003684743ENSE00002196212chr1:154580682-154580468215DSRAD_HUMAN1-550--
1.4dENST000003684744dENSE00001734708chr1:154575102-1545735171586DSRAD_HUMAN6-5345291A:288-366 (gaps)104
1.5ENST000003684745ENSE00001053903chr1:154571061-154570878184DSRAD_HUMAN534-595620--
1.6ENST000003684746ENSE00001053914chr1:154570452-154570304149DSRAD_HUMAN596-645500--
1.7ENST000003684747ENSE00001174669chr1:154569743-154569599145DSRAD_HUMAN645-693490--
1.8aENST000003684748aENSE00001053911chr1:154569471-154569281191DSRAD_HUMAN694-757640--
1.9bENST000003684749bENSE00001053906chr1:154562885-154562660226DSRAD_HUMAN757-832760--
1.10ENST0000036847410ENSE00001053908chr1:154562404-154562233172DSRAD_HUMAN833-890580--
1.11ENST0000036847411ENSE00001053913chr1:154561938-15456184594DSRAD_HUMAN890-921320--
1.12aENST0000036847412aENSE00001200522chr1:154561149-154561027123DSRAD_HUMAN921-962420--
1.12dENST0000036847412dENSE00001174692chr1:154560734-154560601134DSRAD_HUMAN962-1007460--
1.13aENST0000036847413aENSE00001174687chr1:154558839-154558657183DSRAD_HUMAN1007-1068620--
1.14aENST0000036847414aENSE00001174682chr1:154558341-154558229113DSRAD_HUMAN1068-1105380--
1.15bENST0000036847415bENSE00001174679chr1:154557820-154557693128DSRAD_HUMAN1106-1148430--
1.16cENST0000036847416cENSE00001880831chr1:154557519-1545545432977DSRAD_HUMAN1148-1226790--

(-) 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:79
 aligned with DSRAD_HUMAN | P55265 from UniProtKB/Swiss-Prot  Length:1226

    Alignment length:104
                                   272       282       292       302       312       322       332       342       352       362    
          DSRAD_HUMAN   263 DSHSQGSPNSDPGLEPEDSNSTSALEDPLEFLDMAEIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQGTTPPIWHLTDKKRERMQIK 366
               SCOP domains -------------------------------d1xmka1 A:294-366                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------z-alpha-1xmkA01 A:295-359                                        ------- Pfam domains
         Sec.struct. author .....h-------------------------hhhhhhhhhhhhhhhhh..eehhhhhhhhh..hhhhhhhhhhhhhhh..eeee.....eeeehhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------DRADA_REPEAT  PDB: A:294-360 UniProt: 293-360                       ------ PROSITE
               Transcript 1 Exon 1.4d  PDB: A:288-366 (gaps) UniProt: 6-534 [INCOMPLETE]                                             Transcript 1
                 1xmk A 288 GSHMAS-------------------------LDMAEIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQGTTPPIWHLTDKKRERMQIK 366
                                 |   -         -         - |     302       312       322       332       342       352       362    
                               293                       294                                                                        

   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  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (43, 43)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DSRAD_HUMAN | P55265)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004000    adenosine deaminase activity    Catalysis of the reaction: adenosine + H2O = inosine + NH3.
    GO:0003726    double-stranded RNA adenosine deaminase activity    Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a double-stranded RNA molecule.
    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: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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0006382    adenosine to inosine editing    The conversion of an adenosine residue to inosine in an RNA molecule by deamination.
    GO:0016553    base conversion or substitution editing    Any base modification or substitution events that result in alterations in the coding potential or structural properties of RNAs as a result of changes in the base-pairing properties of the modified ribonucleoside(s).
    GO:0098586    cellular response to virus    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 a stimulus from a virus.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0060216    definitive hemopoiesis    A second wave of blood cell production that, in vertebrates, generates long-term hemopoietic stem cells that continously provide erythroid, myeloid and lymphoid lineages throughout adulthood.
    GO:0030218    erythrocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0002244    hematopoietic progenitor cell differentiation    The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
    GO:0061484    hematopoietic stem cell homeostasis    Any biological process involved in the maintenance of the steady-state number of hematopoietic stem cells within a population of cells.
    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:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0035280    miRNA loading onto RISC involved in gene silencing by miRNA    The transfer of a microRNA (miRNA) strand from a miRNA:miRNA duplex onto the RNA-initiated silencing complex (RISC).
    GO:1900369    negative regulation of RNA interference    Any process that stops, prevents or reduces the frequency, rate or extent of RNA interference.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0044387    negative regulation of protein kinase activity by regulation of protein phosphorylation    The stopping, prevention, or reduction in frequency, rate or extent of protein kinase activity as a result of regulating the phosphorylation status of that protein kinase.
    GO:0060339    negative regulation of type I interferon-mediated signaling pathway    Any process that decreases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
    GO:0045071    negative regulation of viral genome replication    Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:0045070    positive regulation of viral genome replication    Any process that activates or increases the frequency, rate or extent of viral genome replication.
    GO:0031054    pre-miRNA processing    Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
    GO:0035196    production of miRNAs involved in gene silencing by miRNA    Cleavage of stem-loop RNA precursors into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein.
    GO:0006611    protein export from nucleus    The directed movement of a protein from the nucleus into the cytoplasm.
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    GO:0035455    response to interferon-alpha    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-alpha stimulus. Interferon-alpha is a type I interferon.
    GO:0009615    response to virus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
    GO:0002566    somatic diversification of immune receptors via somatic mutation    The process in which immune receptor genes are diversified through somatic mutation.
    GO:0060337    type I interferon signaling pathway    A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0044530    supraspliceosomal complex    Multicomponent complex of RNA and proteins that is composed of four active spliceosomes, termed native spliceosomes, connected to each other by the pre-mRNA. The supraspliceosome is the nuclear machine where the pre-mRNA processing takes place, like the 5'-end capping, 3'-end cleavage, splicing and editing.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DSRAD_HUMAN | P552651qbj 1qgp 2acj 2gxb 2l54 2mdr 3f21 3f22 3f23 3irq 3irr

(-) Related Entries Specified in the PDB File

1oyi SOLUTION STRUCTURE OF THE Z-DNA BINDING DOMAIN OF THE VACCINIA VIRUS GENE E3L
1qbj CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX
1qgp NMR STRUCTURE OF THE Z-ALPHA DOMAIN OF ADAR1