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(-) Description

Title :  CRYSTAL STRUCTURE OF CHICKEN MDA5 WITH 5'P 10-MER DSRNA AND ADP-MG2+ AT 2.95 A RESOLUTION (UNTWINNED).
 
Authors :  S. Cusack, E. Uchikawa
Date :  15 Apr 16  (Deposition) - 01 Jun 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B,U,V,X,Y
Biol. Unit 1:  A,X,Y  (1x)
Biol. Unit 2:  B,U,V  (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 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 AND CTD DOMAINS
 
Molecule 2 - RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3')
    Chains: X, Y, U, V
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC DSRNA OBTAINED BY IN VITRO T7 TRANSCRIPTION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABUVXY
Biological Unit 1 (1x): A   XY
Biological Unit 2 (1x):  BUV  

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
1AC1SOFTWARECYS A:881 , CYS A:884 , CYS A:936 , CYS A:939binding site for residue ZN A 1001
2AC2SOFTWARETHR A:300 , ARG A:302 , GLN A:305 , GLY A:325 , SER A:326 , GLY A:327 , LYS A:328 , THR A:329 , ARG A:330 , GLU A:369 , MG A:1003binding site for residue ADP A 1002
3AC3SOFTWARETHR A:329 , ADP A:1002binding site for residue MG A 1003
4AC4SOFTWARECYS B:881 , CYS B:884 , CYS B:936 , CYS B:939binding site for residue ZN B 1001
5AC5SOFTWARETHR 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 , MG B:1003binding site for residue ADP B 1002
6AC6SOFTWARETHR B:329 , ADP B:1002binding site for residue MG B 1003

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JCH)

(-) 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:661
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh....eeee........hhhhhhhhh.eeeeehhhhhhhhhh...hhhhh.eeeee.hhhh...hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhhhhhhhh..eeee............hhhhhhhhhhhhhhh...eeee.hhhh.........eeeee....hhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee.....eeee...eeee...eeee....hhh.eeee......eeee.....eeeeeee....eeeee....eeeee...ee...hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jch A 298 DLTLRDYQMEVAKPALNGENIIICLPTGSGKTRVAVYITKDHLDKKRKASEQGKVIVLVNKVPLVEQHLRKEFNPFLKHWYQVIGLSGDSELKISFPEVVKRYDVIICTAQILENSLLNESVRLSDFSLIIIDQCHHTQKEGVYNNIMRRYLKEKIKNRKQAKELIPQPQILGLTASPGVGGARSNSKAEEHILKICANLDACRIMTVKEHASQLKNQVKEPFKKTVIADDKRRDPFRERIIEIMQDIQKYCQLYPKSEFGSQPYEQWVIREERRAAKEEKRKERVCAEHLKKYNDALQINDTIRMVDAYNHLNNFYKELKRRKTAESDDSKQDETDEFLMRLFHAKKKQLKELARKPEYDNEKLMKLRNTLMEEFTKTEEPRGIIFTKTRQSALALYHWIMDNPKFEEVGIKAHFLIGAGHNSETKPMTQNEQREVIDKFRGGSINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADESTYALVASSGSGAVEREDVNIFRENMMYKAIRRVQEMPPEEYLNKIQDFQLQSIVEKQMKAKRDQRKKNPSLITFLCKNCHKLICSGEDIQVIENMHHVSVKKDFQHLYHKRENQTNVEIICKDCGQVWGNMMVYRGLDLPCLKIRNFVVAFEDTKEIFKKWGELPIIFPD 988
                                   307       317       327       337       347       357       367       377       387       397       407       422       432       442       452       462   ||  475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635|      651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861     ||874       884       894       904       914   ||  934       944       954       964   ||  977       987 
                                                                                                                                                416|                                         466|                                                                                                                                                                  635|                                                                                                                                                                                                                              867|                                            918|                                    968|                
                                                                                                                                                 422                                          470                                                                                                                                                                   642                                                                                                                                                                                                                               871                                             929                                     972                


Chain B from PDB  Type:PROTEIN  Length:655
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh....eeee........hhhhhhhhh.eeeeehhhhhhhhhh...hhhhh.eeeee.hhhh...hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhhhhhhhh..eeee............hhhhhhhhhhhhhhh...eeee.hhhh.........eeeee....hhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeee...eeee...eeee....hhh.eeee......eeee.....eeeeeee....eeeee....eeee....ee...hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jch B 298 DLTLRDYQMEVAKPALNGENIIICLPTGSGKTRVAVYITKDHLDKKRKASEQGKVIVLVNKVPLVEQHLRKEFNPFLKHWYQVIGLSGDSELKISFPEVVKRYDVIICTAQILENSLLNESVRLSDFSLIIIDQCHHTQKEGVYNNIMRRYLKEKIKNRKQAKELIPQPQILGLTASPGVGGARSNSKAEEHILKICANLDACRIMTVKEHASQLKNQVKEPFKKTVIADDKRRDPFRERIIEIMQDIQKYCQLYPKSEFGSQPYEQWVIREERRAAKEEKRKERVCAEHLKKYNDALQINDTIRMVDAYNHLNNFYKELKRRKTAESDDSKQDETDEFLMRLFHAKKKQLKELARKPEYDNEKLMKLRNTLMEEFTKTEEPRGIIFTKTRQSALALYHWIMDNPKFEEVGIKAHFLIGAGHNSETKPMTQNEQREVIDKFRGGSINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADESTYALVASSGSGAVEREDVNIFRENMMYKAIRRVQEMPPEEYLNKIQDFQLQSIVEKQMKAKRDQRITFLCKNCHKLICSGEDIQVIENMHHVSVKKDFQHLYHKRENQTNVEIICKDCGQVWGNMMVYRGLDLPCLKIRNFVVAFEDTKEIFKKWGELPIIFPD 988
                                   307       317       327       337       347       357       367       377       387       397       407       422       432       442       452       462   ||  475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635|      651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861     ||880       890       900       910       930       940       950       960       973       983     
                                                                                                                                                416|                                         466|                                                                                                                                                                  635|                                                                                                                                                                                                                              867|                                      918|                                    968|                
                                                                                                                                                 422                                          470                                                                                                                                                                   642                                                                                                                                                                                                                               877                                       929                                     972                


Chain U from PDB  Type:RNA  Length:10
                                          
                 5jch U   1 GGUACGUACC  10
                                    10


Chain V from PDB  Type:RNA  Length:10
                                          
                 5jch V   1 GGUACGUACC  10
                                    10


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


Chain Y from PDB  Type:RNA  Length:10
                                          
                 5jch Y   1 GGUACGUACC  10
                                    10
   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 5JCH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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        D9N195_CHICK | D9N195: 5jc3 5jc7 5jcf

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