POP-OUT | CLOSE
 
Structural Basis for dsRNA duplex backbone recognition by MDA5
Biology and Chemistry Report
4GL2
  •   Structure Details   Hide

    Structure Keywords

    Keywords RNA BINDING PROTEIN/RNA
    Text MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerization, helicase, ATPase, filament formation, RNA BINDING PROTEIN-RNA complex

    Polymeric Molecules

    Chain A,B
    Description Interferon-induced helicase C domain-containing protein 1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 80468.1 
    Source Method genetically manipulated  
    Entity Name 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 
    Chain C,E
    Description RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polyribonucleotide 
    Formula Weight 3763.3 
    Source Method synthetic  
    Chain D,F
    Description RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polyribonucleotide 
    Formula Weight 3906.4 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ANP  PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER  C10 H17 N6 O12 P3   506.20  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B IFIH1_HUMAN Q2NKL6     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  3.6.4.13      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    16787   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. 
    16817   Hydrolase Activity Acting On Acid Anhydrides  Catalysis of the Hydrolysis of Any Acid Anhydride. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene ifih1, mda5, rh116
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    2 2q24 64135     interferon induced with helicase C domain 1 IFIH1    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs141848057 LS-SNP   dbSNP   A 330 P - > S Coil 20% (Intermediate) 2 163144752 ANP
    rs76332728 LS-SNP   dbSNP   A 340 V - > G Helix 6% (Buried) 2 163144721
    rs183412282 LS-SNP   dbSNP   A 347 L - > F Helix 0% (Buried) 2 163144699
    rs72650664 LS-SNP   dbSNP   A 349 K - > R Helix 40% (Exposed) 2 163144694
    rs35207787 LS-SNP   dbSNP   A 351 K - > E Helix 56% (Exposed) 2 163144689
    rs150317197 LS-SNP   dbSNP   A 356 P - > T Coil 71% (Exposed) 2 163144674
    rs117608083 LS-SNP   dbSNP   A 365 K - > E Coil 22% (Intermediate) 2 163144647
    rs140977021 LS-SNP   dbSNP   A 366 V - > E Bend 42% (Exposed) 2 163139085
    rs145520044 LS-SNP   dbSNP   A 374 R - > H Helix 81% (Exposed) 2 163139061
    rs113854430 LS-SNP   dbSNP   A 374 R - > C Helix 81% (Exposed) 2 163139062
    rs138611889 LS-SNP   dbSNP   A 386 R - > H Coil 80% (Exposed) 2 163139025
    rs111797285 LS-SNP   dbSNP   A 404 V - > A Helix 10% (Intermediate) 2 163138971
    rs148540097 LS-SNP   dbSNP   A 408 D - > N Bend 18% (Intermediate) 2 163138960
    rs201917037 LS-SNP   dbSNP   A 414 A - > P Helix 0% (Buried) 2 163138942
    rs139714761 LS-SNP   dbSNP   A 438 S - > P Bend 12% (Intermediate) 2 163138050
    rs201525208 LS-SNP   dbSNP   A 438 S - > C Bend 12% (Intermediate) 2 163138049
    rs35329951 LS-SNP   dbSNP   A 442 I - > V Beta Ladder 0% (Buried) 2 163138038
    rs147642994 LS-SNP   dbSNP   A 452 A - > V Beta 35% (Intermediate) 2 163138007
    rs10930046 LS-SNP   dbSNP   A 460 H - > R Helix 19% (Intermediate) 2 163137983
    rs190032248 LS-SNP   dbSNP   A 460 H - > Y Helix 19% (Intermediate) 2 163137984
    rs141748480 LS-SNP   dbSNP   A 486 G - > A Beta Ladder 0% (Buried) 2 163137905
    rs147000317 LS-SNP   dbSNP   A 494 G - > V Coil 55% (Exposed) 2 163137881
    rs186791033 LS-SNP   dbSNP   A 499 Q - > P Helix 39% (Exposed) 2 163137866
    rs145641024 LS-SNP   dbSNP   A 520 T - > A Coil 20% (Intermediate) 2 163136589
    rs142348767 LS-SNP   dbSNP   A 528 L - > R Helix 5% (Buried) 2 163136564
    rs111732322 LS-SNP   dbSNP   A 556 E - > K Helix 56% (Exposed) 2 163134814
    rs138057665 LS-SNP   dbSNP   A 575 T - > A Bend 37% (Exposed) 2 163134757
    rs145792185 LS-SNP   dbSNP   A 589 A - > D Helix 0% (Buried) 2 163134203
    rs150760072 LS-SNP   dbSNP   A 589 A - > T Helix 0% (Buried) 2 163134715
    rs74162084 LS-SNP   dbSNP   A 595 R - > H Turn 26% (Intermediate) 2 163134185
    rs191839015 LS-SNP   dbSNP   A 595 R - > S Turn 26% (Intermediate) 2 163134186
    rs200945986 LS-SNP   dbSNP   A 598 R - > H Helix 0% (Buried) 2 163134176
    rs200741709 LS-SNP   dbSNP   A 598 R - > C Helix 0% (Buried) 2 163134177
    rs200017837 LS-SNP   dbSNP   A 618 R - > Q Coil 10% (Intermediate) 2 163134116
    rs186942719 LS-SNP   dbSNP   A 622 A - > V Helix 0% (Buried) 2 163134104
    rs145818112 LS-SNP   dbSNP   A 629 F - > L Helix 21% (Intermediate) 2 163134084
    rs200980825 LS-SNP   dbSNP   A 629 F - > S Helix 21% (Intermediate) 2 163134083
    rs199818504 LS-SNP   dbSNP   A 630 Y - > H Helix 3% (Buried) 2 163134081
    rs189782013 LS-SNP   dbSNP   A 690 L - > P Helix 51% (Exposed) 2 163133432
    rs72650663 LS-SNP   dbSNP   A 702 T - > I Bend 58% (Exposed) 2 163133396
    rs185928139 LS-SNP   dbSNP   A 705 R - > S Helix 33% (Intermediate) 2 163133386
    rs201841403 LS-SNP   dbSNP   A 713 T - > S Helix 92% (Exposed) 2 163133363
    rs200251981 LS-SNP   dbSNP   A 733 A - > V Helix 1% (Buried) 2 163133303
    rs201142986 LS-SNP   dbSNP   A 744 F - > L Coil 26% (Intermediate) 2 163133269
    rs148369169 LS-SNP   dbSNP   A 788 A - > T Beta Ladder 0% (Buried) 2 163130397
    rs141366758 LS-SNP   dbSNP   A 795 G - > S Turn 10% (Intermediate) 2 163130376
    rs144341455 LS-SNP   dbSNP   A 806 R - > C Beta Ladder 1% (Buried) 2 163130343
    rs199638804 LS-SNP   dbSNP   A 812 N - > S Coil 45% (Exposed) 2 163130324
    rs200810568 LS-SNP   dbSNP   A 819 A - > D Helix 0% (Buried) 2 163128896
    rs74162087 LS-SNP   dbSNP   A 820 R - > H Helix 6% (Buried) 2 163128893
    rs201027557 LS-SNP   dbSNP   A 829 T - > P Beta Ladder 8% (Buried) 2 163128867
    rs79324540 LS-SNP   dbSNP   A 842 E - > K Helix 75% (Exposed) 2 163128828
    rs3747517 LS-SNP   dbSNP   A 843 H - > R Helix 43% (Exposed) 2 163128824
    rs138373022 LS-SNP   dbSNP   A 854 M - > R Helix 0% (Buried) 2 163128791
    rs200833729 LS-SNP   dbSNP   A 866 P - > L Helix 54% (Exposed) 2 163128755
    rs143054245 LS-SNP   dbSNP   A 867 E - > G Helix 72% (Exposed) 2 163128752
    rs35667974 LS-SNP   dbSNP   A 923 I - > V Beta Ladder 14% (Intermediate) 2 163124637
    rs140562355 LS-SNP   dbSNP   A 929 V - > I Beta Ladder 1% (Buried) 2 163124619
    rs202009944 LS-SNP   dbSNP   A 965 G - > S Bend 4% (Buried) 2 163123994
    rs74162090 LS-SNP   dbSNP   A 988 V - > L Beta Ladder 1% (Buried) 2 163123826