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(-) Description

Title :  DENGUE VIRUS FULL LENGTH NS5 COMPLEXED WITH VIRAL CAP 0-RNA AND SAH
 
Authors :  Y. Zhao, T. S. Soh, S. P. Lim, K. Y. Chung, K. Swaminathan, S. G. Vasudevan Y. Shi, J. Lescar, D. Luo
Date :  18 Sep 15  (Deposition) - 25 Nov 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dengue Virus, Nonstructural Protein 5, 2'Omtase, Cap0 Rna, Innate Immunity Evasion, Viral Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhao, T. S. Soh, S. P. Lim, K. Y. Chung, K. Swaminathan, S. G. Vasudevan, P. -Y. Shi, J. Lescar, D. Luo
Molecular Basis For Specific Viral Rna Recognition And 2'-O-Ribose Methylation By The Dengue Virus Nonstructural Protein 5 (Ns5)
Proc. Natl. Acad. Sci. Usa V. 112 14834 2015
PubMed-ID: 26578813  |  Reference-DOI: 10.1073/PNAS.1514978112

(-) Compounds

Molecule 1 - NS5
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2496-3385
    Organism Scientific: DENGUE VIRUS 3
    Organism Taxid: 11069
 
Molecule 2 - RNA (5'-R(P*AP*GP*UP*U)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: DENGUE VIRUS
    Organism Taxid: 12637
    Other Details: CAP0 VIRAL RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2M7G1Ligand/Ion7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
5ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:437 , HIS A:441 , CYS A:446 , CYS A:449binding site for residue ZN A 1001
2AC2SOFTWAREHIS A:712 , HIS A:714 , CYS A:728 , CYS A:847binding site for residue ZN A 1002
3AC3SOFTWARESER A:56 , GLY A:58 , GLY A:81 , CYS A:82 , GLY A:85 , GLY A:86 , TRP A:87 , THR A:104 , LYS A:105 , HIS A:110 , GLU A:111 , LYS A:130 , ASP A:131 , VAL A:132 , PHE A:133 , ASP A:146 , HOH A:1118 , HOH A:1255 , A B:1 , G B:2 , HOH B:202 , HOH B:211binding site for residue SAH A 1003
4AC4SOFTWAREASP A:533 , ASP A:664 , HOH A:1144 , HOH A:1145 , HOH A:1160 , HOH A:1301binding site for residue MG A 1004
5AC5SOFTWAREGLU A:428 , ARG A:499 , LYS A:656 , HOH A:1246binding site for residue ACT A 1005
6AC6SOFTWARELYS A:14 , LEU A:17 , ASN A:18 , LEU A:20 , PHE A:25 , LYS A:29 , SER A:151 , PRO A:152 , ARG A:211 , SER A:213 , THR A:214 , A B:1 , MG B:102 , HOH B:201 , HOH B:203 , HOH B:204 , HOH B:205 , HOH B:207binding site for residue M7G B 0
7AC7SOFTWAREM7G B:0 , A B:1 , HOH B:201 , HOH B:205 , HOH B:207binding site for residue MG B 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:742 -Gly A:743
2Gly A:745 -Trp A:746

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DTO)

(-) 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:852
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..hhhhhhhhh....eee.hhhhhhhhhh.........hhhhhhhhhhhh......eeeeee....hhhhhhhh....eeeeeee................hhh.eeee...hhhhh......eeee.......hhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.eee...........eeee.....hhhhhhhhhhhhhhhhhhh.....eee..........hhhhh....hhhhhhhhhhhhhhhh...............eeeeeeee..........hhhhhhhhhhhhh............hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.......eee...hhhhhhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhhhhhh.eeee..eeee....hhhhh.hhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..........................hhhhhhhhhhh.....................hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dto A   6 GETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAVSRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTVEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVRNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVDLGAGTRHVNAEPETPNMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYHGSYEVKATGSASSMINGVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTPRPLPGTRKVMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTNAQWDSAKAAVEDEEFWKLVDRERELHKLGKCGSCVYNMMRAIWYMWLGVRYLEFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHNEEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPTGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKADLENPHLLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSIRETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWENVPYLGKREDQWCGSLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYM 883
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405||     425       435       445       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881  
                                                                                                                                                                                                                                                                                                                                                                                                                                          406|                                  454|                                                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                           417                                   471                                                                                                                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:RNA  Length:4
                                    
                 5dto B   1 AGUU   4
   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 5DTO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 90)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:742 - Gly A:743   [ RasMol ]  
    Gly A:745 - Trp A:746   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q6DLV0_9FLAV | Q6DLV0: 3j6s 3j6t 3j6u
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        Q6DLV0_9FLAV | Q6DLV0: 2j7u 2j7w 3vws 4c11 4hhj 4v0q 4v0r 5eiw 5f3t 5f3z 5f41 5hmw 5hmx 5hmy 5hmz 5hn0 5i3p 5i3q 5iq6 5jjr 5jjs

(-) Related Entries Specified in the PDB File

4v0q DENGUE VIRUS FULL LENGTH NS5 COMPLEXED WITH SAH
4v0r DENGUE VIRUS FULL LENGTH NS5 COMPLEXED WITH GTP AND SAH