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(-) Description

Title :  CRYSTAL STRUCTURE OF CHICKEN LGP2 WITH 5'PPP 10-MER DSRNA AND ADP-ALF4-MG2+ AT 2.2 A RESOLUTION.
 
Authors :  S. Cusack, E. Uchikawa
Date :  13 Apr 16  (Deposition) - 01 Jun 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
 
Molecule 2 - RNA (5'-R(*GPPP*GP*UP*AP*CP*GP*UP*AP*CP*CP*C)-3')
    Chains: X
    Engineered: YES
    Mutation: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC RNA WITH 5' TRIPHOSPHATE
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(*GPPP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3')
    Chains: Y
    Engineered: YES
    Mutation: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC RNA WITH 5' TRIPHOSPHATE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ALF1Ligand/IonTETRAFLUOROALUMINATE ION
3GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
4MG2Ligand/IonMAGNESIUM ION
5ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
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 , HOH A:804 , HOH A:828 , HOH A:869 , HOH A:934 , HOH A:935 , HOH A:999binding site for residue ADP A 702
3AC3SOFTWARETHR A:26 , GLY A:27 , LYS A:30 , GLU A:132 , GLY A:442 , ARG A:469 , ARG A:471 , ADP A:702 , MG A:704 , HOH A:817 , HOH A:819 , HOH A:852 , HOH A:934 , HOH A:988binding site for residue ALF A 703
4AC4SOFTWAREADP A:702 , ALF A:703 , HOH A:819 , HOH A:828 , HOH A:934binding site for residue MG A 704
5AC5SOFTWAREHOH A:812 , GTP X:1 , G X:2 , HOH X:215 , HOH X:224binding site for residue MG X 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JB2)

(-) 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 5JB2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JB2)

(-) Exons   (0, 0)

(no "Exon" information available for 5JB2)

(-) 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:670
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhh..eeeeehhhhhhhhhh.......hhhhh.eeee.hhhhh...hhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhhhhh...eee....hhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh..........eeee............hhhhhhhhhhhhhh....eeee.hhhh.........eeeee....hhhhhhhhhh.......eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhh.eeee.....eeee...eeee...eeee...hhhh.eee.............eeeeeeeee.....eeeeeeee..eeeeee....eeee....ee...............hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jb2 A   1 SELHGYQLEAVAPALRGRNSIVWLPTGAGKTRAAVHVCRRHLEGRRGGRVAVLVNKVHLVQQHLEKEFHVLRDAFKVTAVSGDSSHKCFFGQLAKGSDVVICTAQILQNALLSGEEEARVELTDFSLLVIDECHHTQKEAVYNKIMLSYLQKKLSGQRDLPQILGLTASPGTGGETSFEGAVEHILQICANLDTEVIASAQEHAQHLQSHVPQPTKQYDLCQEREQDPFGQRLKKIMAQIQEHMEMPELPQNFGTQVYEQRIVELENRAAERFCRKTRVCALHLRRYNDALLINDTVRMMDAFQCLQQFYADKKDPTERFLATTFEENRATLQALAGDQRYENPRLSKLEEILQEHFQPPGSSRGIVFTKTRQSAHSLLSWLQDTAGLCGQHIRAAVLTGSGHSNQAKGMTQNEQQDVITLFRYGELNLLFSTSVAEEGLDIPECNIVVRYGLMTNEIAMVQAQGRARAQNSMYSVLAKANSREVYREQLNESLVGLMERAIRAVQAMPERKYRLKIVELQRNAVLSWQVKEARSSERRQLHDPDDVYFHCVNCNVAVCRGSDIRTVEAMHHVNINPNFRFYYTVSSGKIHFERTFRDWEPGCRIVCSECRQEWGMEMIYRNVTLPILSIKNFVVVTPDEKKKYKKWSTVTFPIEEFSYLEYCSSTQDES 673
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  ||   323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673
                                                                                                                                                                                                                                                                                                                                                  313|                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                                                                   317                                                                                                                                                                                                                                                                                                                                                                    


Chain X from PDB  Type:RNA  Length:11
                                           
                 5jb2 X   1 xGUACGUACCC  11
                            |       10 
                            1-GTP      


Chain Y from PDB  Type:RNA  Length:10
                                          
                 5jb2 Y   1 xGUACGUACC  10
                            |       10
                            1-GTP
   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 5JB2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JB2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JB2)

(-) 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

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

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