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(-) Description

Title :  STRUCTURAL BASIS FOR DSRNA DUPLEX BACKBONE RECOGNITION BY MDA5
 
Authors :  B. Wu, S. Hur
Date :  13 Aug 12  (Deposition) - 09 Jan 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.56
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Mda5, Dsrna, Anti-Viral Signaling, Rig-I, Mavs, Oligomerization, Helicase, Atpase, Filament Formation, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Wu, A. Peisley, C. Richards, H. Yao, X. Zeng, C. Lin, F. Chu, T. Walz, S. Hur
Structural Basis For Dsrna Recognition, Filament Formation, And Antiviral Signal Activation By Mda5.
Cell(Cambridge, Mass. ) V. 152 276 2013
PubMed-ID: 23273991  |  Reference-DOI: 10.1016/J.CELL.2012.11.048

(-) Compounds

Molecule 1 - INTERFERON-INDUCED HELICASE C DOMAIN-CONTAINING PROTEIN 1
    Chains: A, B
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: IFIH1, MDA5, RH116
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CLINICALLY AMYOPATHIC DERMATOMYOSITIS AUTOANTIGEN 140 KDA, CADM-140 AUTOANTIGEN, HELICASE WITH 2 CARD DOMAINS, HELICARD, INTERFERON-INDUCED WITH HELICASE C DOMAIN PROTEIN 1, MELANOMA DIFFERENTIATION-ASSOCIATED PROTEIN 5, MDA-5, MURABUTIDE DOWN- REGULATED PROTEIN, RIG-I-LIKE RECEPTOR 2, RLR-2, RNA HELICASE-DEAD BOX PROTEIN 116
 
Molecule 2 - RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3')
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3')
    Chains: F, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:307 , ARG A:309 , GLN A:312 , GLY A:332 , GLY A:334 , LYS A:335 , THR A:336 , ARG A:337BINDING SITE FOR RESIDUE ANP A 1101
2AC2SOFTWARECYS A:907 , CYS A:910 , CYS A:962 , CYS A:964BINDING SITE FOR RESIDUE ZN A 1102
3AC3SOFTWAREGLN B:307 , GLN B:312 , GLY B:332 , CYS B:333 , LYS B:335 , THR B:336 , ARG B:337 , GLU B:376 , ASP B:443 , ASP B:797BINDING SITE FOR RESIDUE ANP B 1101
4AC4SOFTWARECYS B:907 , ASN B:909 , CYS B:910 , CYS B:962 , CYS B:964BINDING SITE FOR RESIDUE ZN B 1102

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:565 -B:600

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Val A:453 -Tyr A:454
2Tyr A:454 -Asn A:455
3Ala A:489 -Ser A:490
4Glu A:742 -Lys A:743
5Phe A:744 -Ala A:745
6Arg A:824 -Ala A:825
7Ala A:825 -Asp A:826
8Gly A:837 -Ser A:838
9Ala B:489 -Ser B:490
10Glu B:742 -Lys B:743

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GL2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GL2)

(-) Exons   (0, 0)

(no "Exon" information available for 4GL2)

(-) 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:617
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhh.......ee..hhhhhhhhhhhhhhhhh....eeee....hhhhhhhh..eeeeehhhhhhhh...hhhhh.eeeee.hhhh.......hhhhhhhhhhhhhhhhhh.....eeeee..........hhhhhhhhhhhhhhhhh.........hhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh......ee.............hhhhhhhhhhhhh....eee...............eee....hhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh........eeeee.....eeee.hhheee...eee..hhhhhhhhee..eee.....eeeee.....eee....eeeee....eee...hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gl2 A  306 LQLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSLKISFPEVVKSCDIIISTAQILENSLLGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKVIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCKKFAIADPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKERVCAEHLRKYNEALQINDTIRMIDAYTHLETFYNEEKDKKFLDETDRFLMTLFFENNKMLKRLAENPEKLTKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAAHHLIGAGHSSEFKPMTQNEQKEVISKFRTNLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADESTYVLVAHSGSGVIERETVNDFREKMMYKAIHCVQNMKPEEYAHKILELQMQSIMEKKMKTKPSLITFLCKNCSVLACSGEDIHVIEKMHHVNMTPEFKELYIVRGEIICKCGQAWGTMMVHKLPCLKIRNFVVVFKNNSTKKQYKKWVELPITFPNL 1013
                                   315       325       335       345       355       365       375       385     ||399       409       419  ||   437       447       457       467     ||481       491       501       511       521       531       541 ||    556       566       576       586       596       606       616       626       636 ||    676       686       700       710       720       730       740    || 755       765       775    || 788       798       808       818       828       838       848       858       868       878       888||     908       918       928       938   ||  963       973 ||    986       996      1006       
                                                                                                               391|                       422|                                       473|                                                              543|                                                                                      638|                      694|                                           745|                          780|                                                                                                      889|                                       942|              975|                                  
                                                                                                                396                        431                                        478                                                               549                                                                                       669                       699                                            751                           784                                                                                                       900                                        958               979                                  


Chain B from PDB  Type:PROTEIN  Length:615
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhh.eeeeehhhhhhhh....hhhhh.eeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhhhhh.........hhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh........eee.............hhhhhhhhhhhhhhh...eeee..............eee....hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh................hhhhheee...eee..hhhhhhhhee..eee.....eeeee....eee.hhhh.ee......ee...hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gl2 B  306 LQLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGLKISFPEVVKSCDIIISTAQILENSLLNGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKVIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCKKFAIPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKERVCAEHLRKYNEALQINDTIRMIDAYTHLETFYNEEKDKKFLDETDRFLMTLFFENNKMLKRLAENPNEKLTKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGDESTYVLVAHSGSGVIERETVNDFREKMMYKAIHCVQNMKPEEYAHKILELQMQSIMEKKMKPSLITFLCKNCSVLACSGEDIHVIEKMHHVNMTPEFKELYIVRGEIICKCGQAWGTMMVHLPCLKIRNFVVVFKNNSTKKQYKKWVELPITFPNL 1013
                                   315       325       335       345       355       365       375       385      |398       408       418    || 435       445       455       465       479       489       499       509       519       529       539 ||    556       566       576       586       596       606       616       626       636 ||    676       686       699       709       719       729       739       751       761       771       781||     793       803       813       827       837       847       857       867       877       887|      909       919       929       939  ||   964       974|      988       998      1008     
                                                                                                                392|                        423|                                       473|                                                            541|                                                                                      638|                      694|                                              747|                             782|                                 821|                                                          887|                                       942|             974|                                  
                                                                                                                 396                         431                                        478                                                             549                                                                                       669                       698                                               750                              785                                  826                                                           900                                        958              979                                  


Chain C from PDB  Type:RNA  Length:12
                                             
                4gl2 C    1 AUCCGCGGCCCU   12
                                    10  


Chain D from PDB  Type:RNA  Length:12
                                             
                4gl2 D    1 AGGGCCGCGGAU   12
                                    10  


Chain E from PDB  Type:RNA  Length:12
                                             
                4gl2 E    1 AUCCGCGGCCCU   12
                                    10  


Chain F from PDB  Type:RNA  Length:12
                                             
                4gl2 F    1 AGGGCCGCGGAU   12
                                    10
   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 4GL2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GL2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GL2)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:489 - Ser A:490   [ RasMol ]  
    Ala A:825 - Asp A:826   [ RasMol ]  
    Ala B:489 - Ser B:490   [ RasMol ]  
    Arg A:824 - Ala A:825   [ RasMol ]  
    Glu A:742 - Lys A:743   [ RasMol ]  
    Glu B:742 - Lys B:743   [ RasMol ]  
    Gly A:837 - Ser A:838   [ RasMol ]  
    Phe A:744 - Ala A:745   [ RasMol ]  
    Tyr A:454 - Asn A:455   [ RasMol ]  
    Val A:453 - Tyr A:454   [ RasMol ]  
 
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        IFIH1_HUMAN | Q9BYX4: 2rqb 3b6e 3ga3

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