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(-) Description

Title :  CRYSTAL STRUCTURE OF CHICKEN MDA5 WITH 5'P 10-MER DSRNA AND ADP-MG2+ AT 2.6 A RESOLUTION (ORTHORHOMBIC FORM).
 
Authors :  S. Cusack, E. Uchikawa
Date :  15 Apr 16  (Deposition) - 01 Jun 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,X,Y
Biol. Unit 1:  A,X,Y  (1x)
Biol. Unit 2:  B,C,D  (1x)
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
    Expression System Plasmid: PETM11
    Expression System Strain: ROSETTA 2
    Expression System Taxid: 562
    Gene: MDA5
    Mutation: YES
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Other Details: CHICKEN MDA5 HELICASE AND CTD DOMAINS
 
Molecule 2 - RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3')
    Chains: X, C, D
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Other Details: RNA WITH 5' MONOPHOSPHATE MADE WITH T7 POLYMERASE IN VITRO
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(P*AP*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3')
    Chains: Y
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Other Details: RNA WITH 5' MONOPHOSPHATE MADE WITH T7 POLYMERASE IN VITRO
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDXY
Biological Unit 1 (1x): A   XY
Biological Unit 2 (1x):  BCD  

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:300 , ARG A:302 , GLN A:305 , THR A:324 , GLY A:325 , SER A:326 , GLY A:327 , LYS A:328 , ARG A:330 , ARG A:798 , MG A:1002 , HOH A:1148binding site for residue ADP A 1001
2AC2SOFTWARETHR A:329 , ADP A:1001binding site for residue MG A 1002
3AC3SOFTWARECYS A:881 , CYS A:884 , CYS A:936 , CYS A:939binding site for residue ZN A 1003
4AC4SOFTWARETHR B:300 , ARG B:302 , GLN B:305 , PRO B:323 , THR B:324 , GLY B:325 , SER B:326 , GLY B:327 , LYS B:328 , ARG B:330 , GLU B:369 , ARG B:798 , MG B:1002 , HOH B:1141binding site for residue ADP B 1001
5AC5SOFTWARETHR B:329 , ADP B:1001binding site for residue MG B 1002
6AC6SOFTWARECYS B:881 , CYS B:884 , CYS B:936 , CYS B:939binding site for residue ZN B 1003

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JCF)

(-) 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:660
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh....eeee........hhhhhhhhh.eeeeehhhhhhhhhh......hhhhh.eeeee.hhhh...hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhhhh...eee....hhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhh...eeee.hhhh.........eeeee....hhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeee...eeee...eeee....hhh.eeee......eeee.....eeeeeeee..eeeeee....eeee....ee...hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jcf A 297 GDLTLRDYQMEVAKPALNGENIIICLPTGSGKTRVAVYITKDHLDKKRKASEQGKVIVLVNKVPLVEQHLRKEFNPFLKHWYQVIGLSGDSELKISFPEVVKRYDVIICTAQILENSLLNATEESVRLSDFSLIIIDQCHHTQKEGVYNNIMRRYLKEKIKNRKQAKELIPQPQILGLTASPGVGGARSNSKAEEHILKICANLDACRIMTVKEHASQLKNQVKEPFKKTVIADDKRRDPFRERIIEIMQDIQKYCQLYPKSEFGSQPYEQWVIREERRAAKEEKRKERVCAEHLKKYNDALQINDTIRMVDAYNHLNNFYKELKRRKTAESDDDSKQDETDEFLMRLFHAKKKQLKELARKPEYDNEKLMKLRNTLMEEFTKTEEPRGIIFTKTRQSALALYHWIMDNPKFEEVGIKAHFLIGAGHNSETKPMTQNEQREVIDKFRGGSINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADESTYALVASSGSGAVEREDVNIFRENMMYKAIRRVQEMPPEEYLNKIQDFQLQSIVEKQMKAKRDQRITFLCKNCHKLICSGEDIQVIENMHHVSVKKDFQHLYHKRENQTNVEIICKDCGQVWGNMMVYRGLDLPCLKIRNFVVAFEDTKEIFKKWGELPIIFPD 988
                                   306       316       326       336       346       356       366       376       386       396       406       416  ||   428       438       448       458       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631    || 646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866||     885       895       905       915  ||   935       945       955       965  ||   978       988
                                                                                                                                                    419|                                         466|                                                                                                                                                                   636|                                                                                                                                                                                                                              867|                                      918|                                    968|                
                                                                                                                                                     422                                          470                                                                                                                                                                    642                                                                                                                                                                                                                               877                                       929                                     972                


Chain B from PDB  Type:PROTEIN  Length:660
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh....eeee........hhhhhhhhh.eeeeehhhhhhhhhh.......hhhhh.eeeee.hhhh...hhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhhhh...eee....hhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhh...eeee.hhhh.........eeeee....hhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeee...eeee...eeee....hhh.eeee......eeee.....eeeeeeee..eeeeee....eeee....ee...hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jcf B 297 GDLTLRDYQMEVAKPALNGENIIICLPTGSGKTRVAVYITKDHLDKKRKASEQGKVIVLVNKVPLVEQHLRKEFNPFLKHWYQVIGLSGDSELKISFPEVVKRYDVIICTAQILENSLLNATEDESVRLSDFSLIIIDQCHHTQKEGVYNNIMRRYLKEKIKNRKQAKLIPQPQILGLTASPGVGGARSNSKAEEHILKICANLDACRIMTVKEHASQLKNQVKEPFKKTVIADDKRRDPFRERIIEIMQDIQKYCQLYPKSEFGSQPYEQWVIREERRAAKEEKRKERVCAEHLKKYNDALQINDTIRMVDAYNHLNNFYKELKRRKTAESDDDSKQDETDEFLMRLFHAKKKQLKELARKPEYDNEKLMKLRNTLMEEFTKTEEPRGIIFTKTRQSALALYHWIMDNPKFEEVGIKAHFLIGAGHNSETKPMTQNEQREVIDKFRGGSINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADESTYALVASSGSGAVEREDVNIFRENMMYKAIRRVQEMPPEEYLNKIQDFQLQSIVEKQMKAKRDQRITFLCKNCHKLICSGEDIQVIENMHHVSVKKDFQHLYHKRENQTNVEIICKDCGQVWGNMMVYRGLDLPCLKIRNFVVAFEDTKEIFKKWGELPIIFPD 988
                                   306       316       326       336       346       356       366       376       386       396       406       416  ||   427       437       447       457       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631    || 646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866||     885       895       905       915  ||   935       945       955       965  ||   978       988
                                                                                                                                                    419|                                         465|                                                                                                                                                                   636|                                                                                                                                                                                                                              867|                                      918|                                    968|                
                                                                                                                                                     421                                          470                                                                                                                                                                    642                                                                                                                                                                                                                               877                                       929                                     972                


Chain C from PDB  Type:RNA  Length:10
                                          
                 5jcf C   1 GGUACGUACC  10
                                    10


Chain D from PDB  Type:RNA  Length:10
                                          
                 5jcf D   1 GGUACGUACC  10
                                    10


Chain X from PDB  Type:RNA  Length:10
                                          
                 5jcf X   1 GGUACGUACC  10
                                    10


Chain Y from PDB  Type:RNA  Length:11
                                           
                 5jcf Y   0 AGGUACGUACC  10
                                     9
   Legend:   → Mismatch (orange background)
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  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 5JCF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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        D9N195_CHICK | D9N195: 5jc3 5jc7 5jch

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