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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REGULATORY DOMAIN OF HUMAN LGP2
 
Authors :  D. A. Pippig, J. C. Hellmuth, S. Cui, A. Kirchhofer, K. Lammens, A. Lammens, A. Schmidt, S. Rothenfusser, K. P. Hopfner
Date :  01 Dec 08  (Deposition) - 24 Feb 09  (Release) - 14 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Innate Immunity, Immune Response, Nucleotide-Binding, Coiled Coil, Atp-Binding, Polymorphism, Double-Strand Rna Binding Protein, Helicase, Hydrolase, Cytoplasm, Rna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. A. Pippig, J. C. Hellmuth, S. Cui, A. Kirchhofer, K. Lammens, A. Lammens, A. Schmidt, S. Rothenfusser, K. P. Hopfner
The Regulatory Domain Of The Rig-I Family Atpase Lgp2 Senses Double-Stranded Rna.
Nucleic Acids Res. V. 37 2014 2009
PubMed-ID: 19208642  |  Reference-DOI: 10.1093/NAR/GKP059

(-) Compounds

Molecule 1 - PROBABLE ATP-DEPENDENT RNA HELICASE DHX58
    ChainsA, B, C, D
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentREGULATORY DOMAIN, RESIDUES 537-678
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other Details4 HG PER ASU 5 SO4 PER ASU
    SynonymPROBABLE ATP-DEPENDENT HELICASE LGP2, PROTEIN D11LGP2 HOMOLOG, LGP2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1HG4Ligand/IonMERCURY (II) ION
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2SO42Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:556 , CYS A:559 , CYS A:612 , CYS A:615BINDING SITE FOR RESIDUE HG A1675
2AC2SOFTWARECYS B:556 , CYS B:559 , CYS B:612 , CYS B:615BINDING SITE FOR RESIDUE HG B1679
3AC3SOFTWARECYS D:556 , CYS D:559 , CYS D:612 , CYS D:615BINDING SITE FOR RESIDUE HG D1676
4AC4SOFTWARECYS C:556 , CYS C:559 , CYS C:612 , CYS C:615BINDING SITE FOR RESIDUE HG C1674
5AC5SOFTWAREHIS A:565 , ASN A:581 , ASN A:583 , HOH A:2017BINDING SITE FOR RESIDUE SO4 A1676
6AC6SOFTWAREHIS B:565 , ASN B:581 , ASN B:583 , HOH B:2037BINDING SITE FOR RESIDUE SO4 B1680
7AC7SOFTWAREHIS C:565 , ASN C:581 , ASN C:583 , HOH C:2039BINDING SITE FOR RESIDUE SO4 C1673
8AC8SOFTWAREGLU C:550 , GLN C:553 , HIS C:565 , SER C:567 , HOH C:2040 , HOH C:2041BINDING SITE FOR RESIDUE SO4 C1675
9AC9SOFTWAREHIS D:565 , ASN D:581 , ASN D:583 , HOH D:2016BINDING SITE FOR RESIDUE SO4 D1677

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:668 -C:668
2B:668 -D:668

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W4R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W4R)

(-) Exons   (0, 0)

(no "Exon" information available for 2W4R)

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

    Alignment length:131
                                   553       563       573       583       593       603       613       623       633       643       653       663       673 
          DHX58_HUMAN   544 RQQFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRDPVVINKVFKDWKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENLSD 674
               SCOP domains d2w4ra_ A: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeee.....eeee...eeee...eeee.hhhhhh.eeee.....----....eeeeeeee.....eeeeeeee..eeeeee....eeeee..eee...hhhhh.......hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w4r A 544 RQQFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRDPVV----FKDWKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENLSD 674
                                   553       563       573       583       593  |    603       613       623       633       643       653       663       673 
                                                                              596  601                                                                         

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with DHX58_HUMAN | Q96C10 from UniProtKB/Swiss-Prot  Length:678

    Alignment length:135
                                   553       563       573       583       593       603       613       623       633       643       653       663       673     
          DHX58_HUMAN   544 RQQFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRDPVVINKVFKDWKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENLSDLSLD 678
               SCOP domains d2w4rb_ B: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeee.....eeee...eeeehhheeee.hhhhhh.eeee..----------.eeeeeeee.....eeeeeeee..eeeeee....eeeee..eee...hhhhh.......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w4r B 544 RQQFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRD----------WKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENLSDLSLD 678
                                   553       563       573       583       593         -|      613       623       633       643       653       663       673     
                                                                           593        604                                                                          

Chain C from PDB  Type:PROTEIN  Length:124
 aligned with DHX58_HUMAN | Q96C10 from UniProtKB/Swiss-Prot  Length:678

    Alignment length:130
                                   552       562       572       582       592       602       612       622       632       642       652       662       672
          DHX58_HUMAN   543 QRQQFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRDPVVINKVFKDWKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENL 672
               SCOP domains d2w4rc_ C: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhh.eeee.....eeee...eeee...eeee.hhhhhh.eee...------.....eeeeeeee.....eeeeeeee..eeeeee....eeeee..eee...hhhhh.......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w4r C 543 QRQQFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRD------VFKDWKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENL 672
                                   552       562       572       582       592|      602       612       622       632       642       652       662       672
                                                                            593    600                                                                        

Chain D from PDB  Type:PROTEIN  Length:125
 aligned with DHX58_HUMAN | Q96C10 from UniProtKB/Swiss-Prot  Length:678

    Alignment length:132
                                   553       563       573       583       593       603       613       623       633       643       653       663       673  
          DHX58_HUMAN   544 RQQFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRDPVVINKVFKDWKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENLSDL 675
               SCOP domains d2w4rd_ D: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------RIG-I_C-RD-2w4rD01 D:550-671                                                                                              ---- Pfam domains (1)
           Pfam domains (2) ------RIG-I_C-RD-2w4rD02 D:550-671                                                                                              ---- Pfam domains (2)
           Pfam domains (3) ------RIG-I_C-RD-2w4rD03 D:550-671                                                                                              ---- Pfam domains (3)
           Pfam domains (4) ------RIG-I_C-RD-2w4rD04 D:550-671                                                                                              ---- Pfam domains (4)
         Sec.struct. author ....hhhh.eeee.....eeee...eeee...eeee.hhhhhh.eeee..-------....eeeeeeee.....eeeeeeee..eeeeee....eeee....ee...hhhhh.......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2w4r D 544 RQQFPVEHVQLLCINCMVAVGHGSDLRKVEGTHHVNVNPNFSNYYNVSRD-------FKDWKPGGVISCRNCGEVWGLQMIYKSVKLPVLKVRSMLLETPQGRIQAKKWSRVPFSVPDFDFLQHCAENLSDL 675
                                   553       563       573       583       593       603       613       623       633       643       653       663       673  
                                                                           593     601                                                                          

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W4R)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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.

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 Related Entries

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

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        DHX58_HUMAN | Q96C102rqa 3eqt

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2W4R)