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(-) Description

Title :  CRYSTAL STRUCTURE OF CHICKEN LGP2 WITH 5'P 12-MER DSRNA AT 3.6 A RESOLUTION
 
Authors :  S. Cusack, E. Uchikawa, M. Lethier
Date :  13 Apr 16  (Deposition) - 01 Jun 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.58
Chains :  Asym./Biol. Unit :  A,X,Y
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 - LGP2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    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*GP*CP*GP*CP*UP*AP*CP*C)-3')
    Chains: X, Y
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC RNA 5 PRIME MONO PHOSPHATE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:554 , CYS A:557 , CYS A:610 , CYS A:613binding site for residue ZN A 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:361 -Pro A:362

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JBJ)

(-) 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:627
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhh..eeee........hhhhhhhhh.eeeeehhhhhhhhhh.............eeeee.hhhh...hhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh..........eeee............hhhhhhhhhhhhhh....eeee..............eeee.....hhhhhhhhhh.................hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee.....eeee...eeee...eeee.hhhhhh.eeeeeee...........eeeeeee.....eeeeeeee..eeeeee....eeee....ee...............hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jbj A   1 SELHGYQLEAVAPALRGRNSIVWLPTGAGKTRAAVHVCRRHLEGRRGGRVAVLVNKVHLVQQHLEKEFHVLRDAFKVTAVSGDSSHKCFFGQLAKGSDVVICTAQILQNALLSGEEEARVELTDFSLLVIDECHHTQKEAVYNKIMLSYLQKKLSGQRDLPQILGLTASPGTGGETSFEGAVEHILQICANLDTEVIASAREQDPFGQRLKKIMAQIQEHMEMPELPQNFGTQVYEQRIVELENRAAERFCRKTRVCALHLRRYNDALLINDTVRMMDAFQCLQQFYADKDPTERFLATTFEENRATLQALAGDQRYNPRLSKLEEILQEHFQPPGSSRGIVFTKTRQSAHSLLSWLQDTAGLCGQHIRAAVLTGSGHSNQAKGMTQNEQQDVITLFRYGELNLLFSTSVAEEGLDIPECNIVVRYGLMTNEIAMVQAQGRARAQNSMYSVLAKANLMERAIRAVQAMPERKYRLKIVELQRNAVLSWQVKEARSSERRQLHDPDDVYFHCVNCNVAVCRGSDIRTVEAMHHVNINPNFRFYYTVSSGKIHFERTFRDWEPGCRIVCSECRQEWGMEMIYRNVTLPILSIKNFVVVTPDEKKKYKKWSTVTFPIEEFSYLEYCSSTQ 670
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200|      233       243       253       263       273       283       293       303       313|      327       337      |348       358       368       378       388       398       408       418       428       438       448       458       468       478     ||503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       
                                                                                                                                                                                                                                 200|                                                                                      313|                       344|                                                                                                                                       484|                                                                                                                                                                          
                                                                                                                                                                                                                                  224                                                                                       318                        346                                                                                                                                        500                                                                                                                                                                          


Chain X from PDB  Type:RNA  Length:12
                                            
                 5jbj X   1 GGUAGCGCUACC  12
                                    10  


Chain Y from PDB  Type:RNA  Length:12
                                            
                 5jbj Y  13 GGUAGCGCUACC  24
                                    22
   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 5JBJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gln A:361 - Pro A:362   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

(-) Related Entries Specified in the PDB File

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