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(-) Description

Title :  CRYSTAL STRUCTURE OF CHICKEN MDA5 WITH 5'P 24-MER DSRNA AND ADP-MG2+ AT 2.75 A RESOLUTION.
 
Authors :  S. Cusack, E. Uchikawa
Date :  14 Apr 16  (Deposition) - 01 Jun 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B,X,Y
Keywords :  Innate Immune Pattern Recognition Receptor, Rig-I Like Helicase, Dsrna Dependent Atpase, Zinc-Containing Ctd Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Uchikawa, M. Lethier, H. Malet, J. Brunel, D. Gerlier, S. Cusack
Structural Analysis Of Dsrna Binding To Anti-Viral Pattern Recognition Receptors Lgp2 And Mda5.
Mol. Cell V. 62 586 2016
PubMed-ID: 27203181  |  Reference-DOI: 10.1016/J.MOLCEL.2016.04.021

(-) Compounds

Molecule 1 - MELANOMA DIFFERENTIATION ASSOCIATED PROTEIN-5
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Expression System Vector Type: PETM11
    Gene: MDA5
    Mutation: YES
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Other Details: CHICKEN MDA5 HELICASE-CTD DOMAINS
 
Molecule 2 - RNA (5'- R(P*GP*GP*AP*CP*GP*UP*CP*AP*UP*GP*CP*GP*CP*AP*UP*GP*AP*CP*GP*UP*CP*CP *CP*C)-3')
    Chains: X
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Other Details: SYNTHETIC DSRNA USING T7 POLYMERASE
    Synthetic: YES
 
Molecule 3 - RNA (5'- R(P*GP*GP*GP*AP*CP*GP*UP*CP*AP*UP*GP*CP*GP*CP*AP*UP*GP*AP*CP*GP*UP*CP *CP*C)-3')
    Chains: Y
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Other Details: SYNTHETIC DSRNA USING T7 POLYMERASE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:881 , CYS A:884 , CYS A:936 , CYS A:939binding site for residue ZN A 1001
2AC2SOFTWARETHR A:329 , ADP A:1003binding site for residue MG A 1002
3AC3SOFTWAREARG A:302 , GLN A:305 , PRO A:323 , GLY A:325 , GLY A:327 , LYS A:328 , THR A:329 , ARG A:330 , GLU A:369 , ARG A:798 , MG A:1002 , GLU B:515binding site for residue ADP A 1003
4AC4SOFTWARECYS B:881 , CYS B:884 , CYS B:936 , CYS B:939binding site for residue ZN B 1001
5AC5SOFTWARETHR B:329 , ADP B:1003binding site for residue MG B 1002
6AC6SOFTWARETHR B:300 , ARG B:302 , GLN B:305 , PRO B:323 , GLY B:325 , SER B:326 , GLY B:327 , LYS B:328 , THR B:329 , ARG B:330 , GLU B:369 , ARG B:798 , MG B:1002binding site for residue ADP B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JC7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JC7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JC7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JC7)

(-) Exons   (0, 0)

(no "Exon" information available for 5JC7)

(-) 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:641
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhh....eee.........hhhhhhhhh.eeeeehhhhhhhhhh...hhhhh.eeeee.hhhh...hhhhhhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhhhhhhhhhh..eeee............hhhhhhhhhhhhhhh...eeee.hhhh.........eeee.....hhhhhhhhhhh......eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.....eeee...eeee...eeee........eee...eee.....eeeeeee....eeeee....eeee...ee...hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jc7 A 298 DLTLRDYQMEVAKPALNGENIIICLPTGSGKTRVAVYITKDHLDKKRKASEQGKVIVLVNKVPLVEQHLRKEFNPFLKHWYQVIGLSGDSELKISFPEVVKRYDVIICTAQILENSLLNESVRLSDFSLIIIDQCHHTQKEGVYNNIMRRYLKEKIKNRPQPQILGLTASPGVGGARSNSKAEEHILKICANLDACRIMTVKEHASQLKNQVKEPFKKTVIADDKRRDPFRERIIEIMQDIQKYCQLYPKSEFGSQPYEQWVIREERRAAKEEKRKERVCAEHLKKYNDALQINDTIRMVDAYNHLNNFYKELKRRKTAESSKQDETDEFLMRLFHAKKKQLKELARKPEYDNEKLMKLRNTLMEEFTKTEEPRGIIFTKTRQSALALYHWIMDNPKFEEVGIKAHFLIGAGHNSETKPMTQNEQREVIDKFRGGSINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADESTYALVASSGSGAVEREDVNIFRENMMYKAIRRVQEMPPEEYLNKIQDFQLQSIVEKQMKAKRDQRITFLCKNCHKLICSGEDIQVIENMHHVSVKKDFQHLYHKREEIICKDCGQVWGNMMVYRGLDLPCLKIRNFVVAFETKEIFKKWGELPIIFPDF 989
                                   307       317       327       337       347       357       367       377       387       397       407       422       432       442       452       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632||     650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860      |879       889       899       909       934       944       954       964  ||   978       988 
                                                                                                                                                416|                                    461|                                                                                                                                                              633|                                                                                                                                                                                                                              867|                                     917|                               967|                 
                                                                                                                                                 422                                     472                                                                                                                                                               642                                                                                                                                                                                                                               877                                      933                                972                 


Chain B from PDB  Type:PROTEIN  Length:647
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhh....eee.........hhhhhhhhh.eeeeehhhhhhhhhh...hhhhh.eeeee.hhhh...hhhhhhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhhhhhhhhhh..eeee............hhhhhhhhhhhhhhh...eeee.hhhh.........eeee.....hhhhhhhhhhh......eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.....eeee...eeee...eeee........eee...eee.....eeeeeee....eeeee....eeee....ee...hhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jc7 B 298 DLTLRDYQMEVAKPALNGENIIICLPTGSGKTRVAVYITKDHLDKKRKASEQGKVIVLVNKVPLVEQHLRKEFNPFLKHWYQVIGLSGDSELKISFPEVVKRYDVIICTAQILENSLLNESVRLSDFSLIIIDQCHHTQKEGVYNNIMRRYLKEKIKNRPQPQILGLTASPGVGGARSNSKAEEHILKICANLDACRIMTVKEHASQLKNQVKEPFKKTVIADDKRRDPFRERIIEIMQDIQKYCQLYPKSEFGSQPYEQWVIREERRAAKEEKRKERVCAEHLKKYNDALQINDTIRMVDAYNHLNNFYKELKRRKTAESPLVSKQDETDEFLMRLFHAKKKQLKELARKPEYDNEKLMKLRNTLMEEFTKTEEPRGIIFTKTRQSALALYHWIMDNPKFEEVGIKAHFLIGAGHNSETKPMTQNEQREVIDKFRGGSINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADESTYALVASSGSGAVEREDVNIFRENMMYKAIRRVQEMPPEEYLNKIQDFQLQSIVEKQMKAKRDQRITFLCKNCHKLICSGEDIQVIENMHHVSVKKDFQHLYHKREEIICKDCGQVWGNMMVYRGLDLPCLKIRNFVVAFETTKEIFKKWGELPIIFPDFDY 991
                                   307       317       327       337       347       357       367       377       387       397       407       422       432       442       452       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632||     647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867|      886       896       906       916||     941       951       961     ||974       984       
                                                                                                                                                416|                                    461|                                                                                                                                                              633|                                                                                                                                                                                                                                 867|                                     917|                               967|                    
                                                                                                                                                 422                                     472                                                                                                                                                               639                                                                                                                                                                                                                                  877                                      933                                971                    


Chain X from PDB  Type:RNA  Length:24
                                                        
                 5jc7 X   1 GGACGUCAUGCGCAUGACGUCCCC  24
                                    10        20    


Chain Y from PDB  Type:RNA  Length:24
                                                        
                 5jc7 Y   2 GGGACGUCAUGCGCAUGACGUCCC  25
                                    11        21
   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 5JC7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JC7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JC7)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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UniProtKB/TrEMBL
        D9N195_CHICK | D9N195: 5jc3 5jcf 5jch

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