Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN LGP2 C-TERMINAL DOMAIN IN COMPLEX WITH DSRNA
 
Authors :  P. Li, X. Li
Date :  01 Oct 08  (Deposition) - 10 Mar 09  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Innate Immunity, Rig-I-Like Helicases, Viral Rna Detection, Lgp2/Dsrna Complex, Atp-Binding, Coiled Coil, Cytoplasm, Helicase, Hydrolase, Immune Response, Nucleotide-Binding, Polymorphism, Rna-Binding, Rna Binding Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Li, C. T. Ranjith-Kumar, M. T. Brooks, S. Dharmaiah, A. B. Herr, C. Kao, P. Li
The Rig-I-Like Receptor Lgp2 Recognizes The Termini Of Double-Stranded Rna
J. Biol. Chem. V. 284 13881 2009
PubMed-ID: 19278996  |  Reference-DOI: 10.1074/JBC.M900818200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DHX58
    Chains: A, B
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LGP2 C-TERMINAL DOMAIN (UNP RESIDUES 541 TO 678)
    Gene: D11LGP2E, DHX58, LGP2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROBABLE ATP-DEPENDENT HELICASE LGP2, PROTEIN D11LGP2 HOMOLOG
 
Molecule 2 - 5'-R(*GP*CP*GP*CP*GP*CP*GP*C)-3'
    Chains: C, D
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:556 , CYS A:559 , CYS A:612 , CYS A:615BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWARECYS B:556 , CYS B:559 , CYS B:612 , CYS B:615BINDING SITE FOR RESIDUE ZN B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EQT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EQT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EQT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EQT)

(-) Exons   (0, 0)

(no "Exon" information available for 3EQT)

(-) 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:127
 aligned with DHX58_HUMAN | Q96C10 from UniProtKB/Swiss-Prot  Length:678

    Alignment length:127
                                   555       565       575       585       595       605       615       625       635       645       655       665       
          DHX58_HUMAN   546 QFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRDPVVINKVFKDWKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENL 672
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eeee.....eeee...eeee...eeee.hhhhhh.eee.............eeeeeeeee.....eeeeeeee..eeeeee....eeeee..eee...hhhhh.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eqt A 546 QFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRDPVVINKVFKDWKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENL 672
                                   555       565       575       585       595       605       615       625       635       645       655       665       


Chain B from PDB  Type:PROTEIN  Length:142
 aligned with DHX58_HUMAN | Q96C10 from UniProtKB/Swiss-Prot  Length:678

    Alignment length:142
                                                                                                                                                                678       
                                   553       563       573       583       593       603       613       623       633       643       653       663       673    |    -  
          DHX58_HUMAN   544 RQQFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRDPVVINKVFKDWKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENLSDLSLD-------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeee.....eeee...eeee...eeee.hhhhhh.eee.............eeeeeeeee.....eeeeeeee..eeeeee....eeeee..eee...hhhhh.......hhhhhhhhhh.hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eqt B 544 RQQFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRDPVVINKVFKDWKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENLSDLSLDLEHHHHH 685
                                   553       563       573       583       593       603       613       623       633       643       653       663       673       683  


Chain C from PDB  Type:RNA  Length:8
                                        
                 3eqt C   1 GCGCGCGC   8


Chain D from PDB  Type:RNA  Length:8
                                        
                 3eqt D   1 GCGCGCGC   8
   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  (0, 0)

(no "SCOP Domain" information available for 3EQT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EQT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EQT)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DHX58_HUMAN | Q96C10)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    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).
    GO:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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: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:0039534    negative regulation of MDA-5 signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) MDA-5 (also known as IFIH1) binding to viral RNA.
    GO:0039536    negative regulation of RIG-I signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) RIG-1 (also known as DDX58) binding to viral RNA.
    GO:0045824    negative regulation of innate immune response    Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response.
    GO:0032480    negative regulation of type I interferon production    Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:1900245    positive regulation of MDA-5 signaling pathway    Any process that activates or increases the frequency, rate or extent of MDA-5 signaling pathway.
    GO:1900246    positive regulation of RIG-I signaling pathway    Any process that activates or increases the frequency, rate or extent of RIG-I signaling pathway.
    GO:0032481    positive regulation of type I interferon production    Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0045088    regulation of innate immune response    Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    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:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3eqt)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3eqt
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DHX58_HUMAN | Q96C10
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.6.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DHX58_HUMAN | Q96C10
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DHX58_HUMAN | Q96C10: 2rqa 2w4r

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3EQT)