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(-) Description

Title :  STRUCTURAL BASIS FOR RNA RECOGNITION AND ACTIVATION OF RIG-I
 
Authors :  F. Jiang, M. T. Miller, J. Marcotrigiano
Date :  02 Oct 15  (Deposition) - 18 Nov 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Adenosine Triphosphatases, Adenosine Triphosphate, Dead-Box Rna Helicases, Enzyme Activation, Fluorometry, Humans, Immunity, Innate, Models, Molecular, Nucleic Acid Conformation, Pliability, Protein Binding, Protein Structure, Tertiary, Proteolysis, Rna, Double- Stranded, Rna-Binding Proteins, Scattering, Small Angle, Structure- Activity Relationship, Substrate Specificity, Trypsin, Hydrolase, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Jiang, A. Ramanathan, M. T. Miller, G. Q. Tang, M. Gale, S. S. Patel, J. Marcotrigiano
Structural Basis Of Rna Recognition And Activation By Innat Immune Receptor Rig-I.
Nature V. 479 423 2011
PubMed-ID: 21947008  |  Reference-DOI: 10.1038/NATURE10537

(-) Compounds

Molecule 1 - PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
    Chains: A
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: RIG-I (232-925), RIG-I DELTACARD
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: MODIFIED PET 28A
    Fragment: UNP RESIDUES 232-925
    Gene: DDX58
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEAD BOX PROTEIN 58,RIG-I-LIKE RECEPTOR 1,RLR-1,RETINOIC ACID-INDUCIBLE GENE 1 PROTEIN,RIG-1,RETINOIC ACID-INDUCIBLE GENE I PROTEIN,RIG-I
 
Molecule 2 - RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*U)-3')
    Chains: B, C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

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
2BEF1Ligand/IonBERYLLIUM TRIFLUORIDE ION
3GOL1Ligand/IonGLYCEROL
4MG3Ligand/IonMAGNESIUM ION
5ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:810 , CYS A:813 , CYS A:864 , CYS A:869binding site for residue ZN A 1001
2AC2SOFTWAREARG A:320 , ASN A:341binding site for residue MG A 1002
3AC3SOFTWAREASP A:372 , ADP A:1006 , BEF A:1007binding site for residue MG A 1003
4AC4SOFTWAREASN A:298 , HIS A:381binding site for residue MG A 1004
5AC5SOFTWAREGLY A:257 , ASN A:259 , LEU A:402 , GLN A:404binding site for residue GOL A 1005
6AC6SOFTWAREPHE A:241 , LYS A:242 , ARG A:244 , GLN A:247 , PRO A:265 , THR A:266 , GLY A:267 , GLY A:269 , LYS A:270 , THR A:271 , ASP A:705 , MG A:1003 , BEF A:1007binding site for residue ADP A 1006
7AC7SOFTWARETHR A:266 , LYS A:270 , GLU A:373 , GLU A:702 , MG A:1003 , ADP A:1006binding site for residue BEF A 1007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E3H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E3H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E3H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E3H)

(-) Exons   (0, 0)

(no "Exon" information available for 5E3H)

(-) 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:642
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhh.....eeeehhhhhh..hhhhhhhh..eeeehhhhhhhhhhh....hhhhh.eeeee.hhhh...hhhhhhhhhhhhhhhh.......eeeeee.........hhhhhhhhhhhhhhhh...eee....hhhhhh......eeeeee......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhh.....eeee.hhhh.........eeeee....hhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........eee......eeee...eeee...eeee...hhhh.eeeee...........eeeeeee.....eeeeeeee..eeeeee.hhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5e3h A 241 FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLEFGTQKYEQWIVTVQKACMVFDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGTGMTLPAQKCILDAFKDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDSQEVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARCSHDWGIHVKYKTFEIPVIKIESFTLYSKWKDFHFEKIPFDPAE 922
                                   250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490   ||  509       519   ||  532       542       552       562       572   ||  586       596       606       616       626       636       646       656       671       681    || 694       704       714       724       734       744       754       764       774       784       794||     808       818       828       838       848       858       870       880       890 ||    910       920  
                                                                                                                                                                                                                                                                                       494|                523|                                              576|                                                                                 665|            686|                                                                                                      795|                                                               866|                    892|                   
                                                                                                                                                                                                                                                                                        504                 527                                               581                                                                                  671             690                                                                                                       800                                                                869                     903                   


Chain B from PDB  Type:RNA  Length:12
                                            
                 5e3h B   1 CGACGCUAGCGU  12
                                    10  


Chain C from PDB  Type:RNA  Length:12
                                            
                 5e3h C   3 ACGCUAGCGUCG  14
                                    12
   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 5E3H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E3H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E3H)

(-) Gene Ontology  (46, 46)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  5e3h
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  DDX58_HUMAN | O95786
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  3.6.4.13
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 Related Entries

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

UniProtKB/Swiss-Prot
        DDX58_HUMAN | O95786: 2lwd 2lwe 2qfb 2qfd 2rmj 2ykg 3lrn 3lrr 3ncu 3og8 3zd6 3zd7 4ay2 4bpb 4nqk 4on9 4p4h 5f98 5f9f 5f9h

(-) Related Entries Specified in the PDB File

3tmi THIS ENTRY SUPERSEDES 3TMI