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(-) Description

Title :  STRUCTURE OF CHICKEN LGP2 WITHA 5'P 10-MER DSRNA AND ADP-ALF4-MG.
 
Authors :  S. Cusack, E. Uchikawa
Date :  12 Apr 16  (Deposition) - 01 Jun 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,X,Y
Keywords :  Innate Immune Pattern Recognition Receptor, Rig-I Like Helcase, Dsrna Binding, Dsrna-Dependent Atpase, Rna Binding Protein (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 - LGP2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETM11SUMO
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Mutation: YES
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
 
Molecule 2 - RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*CP*C)-3')
    Chains: X
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3')
    Chains: Y
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ALF1Ligand/IonTETRAFLUOROALUMINATE ION
3EDO3Ligand/Ion1,2-ETHANEDIOL
4MG1Ligand/IonMAGNESIUM ION
5MGF1Ligand/IonTRIFLUOROMAGNESATE
6ZN1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:554 , CYS A:557 , CYS A:610 , CYS A:613binding site for residue ZN A 701
2AC2SOFTWAREGLU A:2 , LEU A:3 , HIS A:4 , GLN A:7 , GLY A:27 , ALA A:28 , GLY A:29 , LYS A:30 , THR A:31 , ARG A:32 , GLU A:67 , ASP A:444 , ARG A:471 , ALF A:703 , MG A:704 , EDO A:705 , HOH A:853 , HOH A:887 , HOH A:922 , HOH A:990 , HOH A:1044binding site for residue ADP A 702
3AC3SOFTWARETHR A:26 , GLY A:27 , LYS A:30 , GLU A:132 , ALA A:168 , GLY A:442 , ARG A:469 , ARG A:471 , ADP A:702 , MG A:704 , HOH A:836 , HOH A:851 , HOH A:872 , HOH A:990 , HOH A:1059binding site for residue ALF A 703
4AC4SOFTWAREADP A:702 , ALF A:703 , HOH A:851 , HOH A:922 , HOH A:990binding site for residue MG A 704
5AC5SOFTWARETHR A:31 , GLN A:62 , HIS A:63 , GLU A:67 , ASP A:444 , ADP A:702binding site for residue EDO A 705
6AC6SOFTWARELYS A:138 , ASN A:143 , LEU A:147 , TRP A:531 , HOH A:892binding site for residue EDO A 706
7AC7SOFTWAREVAL A:196 , ILE A:197 , VAL A:508 , GLN A:509 , HOH A:945binding site for residue EDO A 707
8AC8SOFTWARELYS A:56 , HOH A:987 , HOH A:1235 , G X:6 , HOH X:126 , G Y:6 , U Y:7binding site for residue MGF Y 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JAJ)

(-) 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:653
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhh..eeee........hhhhhhhh..eeeeehhhhhhhhhh.......hhhhh.eeee.hhhhh...hhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhhhhh...eee.....eeeeeee.....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh..........eeee............hhhhhhhhhhhhhh....eeee.hhhh.........eeeee....hhhhhhhhhh.......eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhh.eeee.....eeee...eeee...eeee...hhhh.eeeeeee.........eeeeeeeee.....eeeeeeee..eeeeee....eeee....ee...hhhhh....ee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jaj A   2 ELHGYQLEAVAPALRGRNSIVWLPTGAGKTRAAVHVCRRHLEGRRGGRVAVLVNKVHLVQQHLEKEFHVLRDAFKVTAVSGDSSHKCFFGQLAKGSDVVICTAQILQNALLSGEEEARVELTDFSLLVIDECHHTQKEAVYNKIMLSYLQKKLSGQRDLPQILGLTASPGTGGETSFEGAVEHILQICANLDTEVIASAQQPTKQYDLCQEREQDPFGQRLKKIMAQIQEHMEMPELPQNFGTQVYEQRIVELENRAAERFCRKTRVCALHLRRYNDALLINDTVRMMDAFQCLQQFYADKDPTERFLATTFEENRATLQALAGDQRYENPRLSKLEEILQEHFQGSSRGIVFTKTRQSAHSLLSWLQDTAGLCGQHIRAAVLTGSGHSNQAKGMTQNEQQDVITLFRYGELNLLFSTSVAEEGLDIPECNIVVRYGLMTNEIAMVQAQGRARAQNSMYSVLAKANSREVYREQLNESLVGLMERAIRAVQAMPERKYRLKIVELQRNAVLSWQVKEARSSERRQLHDPDDVYFHCVNCNVAVCRGSDIRTVEAMHHVNINPNFRFYYTVSSGKIHFERTFRDWEPGCRIVCSECRQEWGMEMIYRNVTLPILSIKNFVVVTPDEKKKYKKWSTVTFPIEEFSYLEYCSSTQD 671
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201|      222       232       242       252       262       272       282       292       302       312|      326       336       346       356    || 368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668   
                                                                                                                                                                                                                                 201|                                                                                                312|                                         361|                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                  213                                                                                                 317                                          364                                                                                                                                                                                                                                                                                                                   


Chain X from PDB  Type:RNA  Length:11
                                           
                 5jaj X   1 GGUACGUACCC  11
                                    10 


Chain Y from PDB  Type:RNA  Length:10
                                          
                 5jaj Y   1 GGUACGUACC  10
                                    10
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5JAJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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UniProtKB/TrEMBL
        G0YYQ5_CHICK | G0YYQ5: 5jb2 5jbg 5jbj

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