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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX
 
Authors :  T. Schwartz, M. A. Rould, A. Rich
Date :  22 Apr 99  (Deposition) - 02 Jul 99  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,D,E  (1x)
Biol. Unit 2:  C,F  (2x)
Keywords :  Protein-Z-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Schwartz, M. A. Rould, K. Lowenhaupt, A. Herbert, A. Rich
Crystal Structure Of The Zalpha Domain Of The Human Editing Enzyme Adar1 Bound To Left-Handed Z-Dna.
Science V. 284 1841 1999
PubMed-ID: 10364558  |  Reference-DOI: 10.1126/SCIENCE.284.5421.1841

(-) Compounds

Molecule 1 - DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
    ChainsD, E, F
    EngineeredYES
    Other DetailsSYNTHETIC
    SyntheticYES
 
Molecule 2 - PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainNOVABLUE (DE3)
    Expression System Taxid562
    Expression System VectorPLASMID
    FragmentN-TERMINAL HELIX-TURN-HELIX DOMAIN ZALPHA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB DE 
Biological Unit 2 (2x)  C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1QBJ)

(-) Sites  (0, 0)

(no "Site" information available for 1QBJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr A:191 -Pro A:192
2Thr B:191 -Pro B:192
3Thr C:191 -Pro C:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

Asymmetric Unit (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069535P193ADSRAD_HUMANDisease (AGS6)145588689A/B/CP193A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069535P193ADSRAD_HUMANDisease (AGS6)145588689A/BP193A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069535P193ADSRAD_HUMANDisease (AGS6)145588689CP193A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 3)

Asymmetric Unit (1, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENST000003684743ENSE00002196212chr1:154580682-154580468215DSRAD_HUMAN1-550--
1.4dENST000003684744dENSE00001734708chr1:154575102-1545735171586DSRAD_HUMAN6-5345293A:134-198
B:136-198
C:134-199
65
63
66
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 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:65
 aligned with DSRAD_HUMAN | P55265 from UniProtKB/Swiss-Prot  Length:1226

    Alignment length:65
                                   143       153       163       173       183       193     
          DSRAD_HUMAN   134 SIYQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLWKIA 198
               SCOP domains d1qbja_ A:                                                        SCOP domains
               CATH domains 1qbjA00 A:134-198 'winged helix' repressor DNA binding domain     CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh....eeehhhhhhhh...hhhhhhhhhhhhhh..eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------A----- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.4d  PDB: A:134-198 UniProt: 6-534 [INCOMPLETE]             Transcript 1
                 1qbj A 134 SIYQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLWKIA 198
                                   143       153       163       173       183       193     

Chain B from PDB  Type:PROTEIN  Length:63
 aligned with DSRAD_HUMAN | P55265 from UniProtKB/Swiss-Prot  Length:1226

    Alignment length:63
                                   145       155       165       175       185       195   
          DSRAD_HUMAN   136 YQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLWKIA 198
               SCOP domains d1qbjb_ B:                                                      SCOP domains
               CATH domains 1qbjB00 B:136-198 'winged helix' repressor DNA binding domain   CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....eeehhhhhhhh...hhhhhhhhhhhhhh..eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------A----- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.4d  PDB: B:136-198 UniProt: 6-534 [INCOMPLETE]           Transcript 1
                 1qbj B 136 YQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLWKIA 198
                                   145       155       165       175       185       195   

Chain C from PDB  Type:PROTEIN  Length:66
 aligned with DSRAD_HUMAN | P55265 from UniProtKB/Swiss-Prot  Length:1226

    Alignment length:66
                                   143       153       163       173       183       193      
          DSRAD_HUMAN   134 SIYQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLWKIAV 199
               SCOP domains d1qbjc_ C:                                                         SCOP domains
               CATH domains 1qbjC00 C:134-199 'winged helix' repressor DNA binding domain      CATH domains
           Pfam domains (1) -z-alpha-1qbjC01 C:135-199                                         Pfam domains (1)
           Pfam domains (2) -z-alpha-1qbjC02 C:135-199                                         Pfam domains (2)
           Pfam domains (3) -z-alpha-1qbjC03 C:135-199                                         Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhhhhh....eeehhhhhhhh...hhhhhhhhhhhhhh..eeee.....eeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------A------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.4d  PDB: C:134-199 UniProt: 6-534 [INCOMPLETE]              Transcript 1
                 1qbj C 134 SIYQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLWKIAV 199
                                   143       153       163       173       183       193      

Chain D from PDB  Type:DNA  Length:6
                                      
                 1qbj D   1 CGCGCG   6

Chain E from PDB  Type:DNA  Length:6
                                      
                 1qbj E   1 CGCGCG   6

Chain F from PDB  Type:DNA  Length:6
                                      
                 1qbj F   1 CGCGCG   6

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

Asymmetric Unit

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (43, 43)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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 | P552651qgp 1xmk 2acj 2gxb 2l54 2mdr 3f21 3f22 3f23 3irq 3irr

(-) Related Entries Specified in the PDB File

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