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(-) Description

Title :  WEST NILE VIRUS NON-STRUCTURAL PROTEIN 1 (NS1) FORM 1 CRYSTAL
 
Authors :  D. L. Akey, J. L. Smith
Date :  20 Dec 13  (Deposition) - 19 Feb 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Flavivirus, Non-Structural Protein 1, Ns1, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Akey, W. C. Brown, S. Dutta, J. Konwerski, J. Jose, T. J. Jurkiw, J. Delproposto, C. M. Ogata, G. Skiniotis, R. J. Kuhn, J. L. Smith
Flavivirus Ns1 Structures Reveal Surfaces For Associations With Membranes And The Immune System.
Science V. 343 881 2014
PubMed-ID: 24505133  |  Reference-DOI: 10.1126/SCIENCE.1247749

(-) Compounds

Molecule 1 - NS1
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PH-AC64-7
    Expression System Strain: HIGH FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: NS1
    Organism Common: WNV
    Organism Scientific: WEST NILE VIRUS
    Organism Taxid: 11082
    Strain: NY99
 
Molecule 2 - NS1
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PH-AC64-7
    Expression System Strain: HIGH FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: NS1
    Organism Common: WNV
    Organism Scientific: WEST NILE VIRUS
    Organism Taxid: 11082
    Strain: NY99

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 24)

Asymmetric/Biological Unit (6, 24)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
4OXN4Ligand/IonOXTOXYNOL-10
5SO42Ligand/IonSULFATE ION
6UNK6Mod. Amino Acid

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:130 , THR A:132 , VAL A:134 , GLU A:142 , NAG A:402BINDING SITE FOR RESIDUE NAG A 401
02AC2SOFTWARENAG A:401BINDING SITE FOR RESIDUE NAG A 402
03AC3SOFTWAREPRO A:101 , ASN A:175BINDING SITE FOR RESIDUE NAG A 403
04AC4SOFTWAREASN A:207 , NAG A:405BINDING SITE FOR RESIDUE NAG A 404
05AC5SOFTWARENAG A:404BINDING SITE FOR RESIDUE NAG A 405
06AC6SOFTWAREOXN A:408BINDING SITE FOR RESIDUE OXN A 406
07AC7SOFTWARELEU A:162BINDING SITE FOR RESIDUE OXN A 407
08AC8SOFTWAREOXN A:406BINDING SITE FOR RESIDUE OXN A 408
09AC9SOFTWAREPRO B:101 , ASN B:175 , NAG B:402BINDING SITE FOR RESIDUE NAG B 401
10BC1SOFTWARENAG B:401BINDING SITE FOR RESIDUE NAG B 402
11BC2SOFTWAREASN B:207 , ASP B:208 , NAG B:404BINDING SITE FOR RESIDUE NAG B 403
12BC3SOFTWARELYS B:92 , NAG B:403 , BMA B:405BINDING SITE FOR RESIDUE NAG B 404
13BC4SOFTWAREGLU B:91 , NAG B:404 , MAN B:406 , MAN B:407BINDING SITE FOR RESIDUE BMA B 405
14BC5SOFTWAREBMA B:405BINDING SITE FOR RESIDUE MAN B 406
15BC6SOFTWAREBMA B:405BINDING SITE FOR RESIDUE MAN B 407
16BC7SOFTWAREHIS A:293 , HIS B:293 , HOH B:556BINDING SITE FOR RESIDUE SO4 B 408
17BC8SOFTWAREGLY A:235 , ASP B:234 , GLY B:235 , HOH B:519 , HOH B:521BINDING SITE FOR RESIDUE SO4 B 409
18BC9SOFTWARECYS A:4 , LEU A:13 , THR B:2BINDING SITE FOR RESIDUE OXN B 410

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:15
2A:55 -A:143
3A:179 -A:223
4A:280 -A:329
5A:291 -A:312
6A:313 -A:316
7B:4 -B:15
8B:55 -B:143
9B:179 -B:223
10B:280 -B:329
11B:291 -B:312
12B:313 -B:316

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:318 -Pro A:319
2Leu B:318 -Pro B:319

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O6D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O6D)

(-) Exons   (0, 0)

(no "Exon" information available for 4O6D)

(-) 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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhheeeeeee.hhheeeeeeeeeee....hhhh.eeeee.hhhhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhhhhh....eeee....................eeee........hhh.ee...eeeeeee.....eeeeeee........hhhh.eeeee..eeeee...eeeeeee...eeeeeeee........hhhhh......hhhhh..hhhhh........................eeeee......eeee..........ee..........eeee.......eeeee..eeee...eee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o6d A  -6 LYFQSNADTGCAIDISRQELRCGSGVFIHNDVEAWMDRYKYYPETPQGLAKIIQKAHKEGVCGLRSVSRLEHQMWEAVKDELNTLLKENGVDLSVVVEKQEGMYKSAPKRLTATANNTFVVDGPETKECPTQNRAWNSLEVEDFGFGLTSTRMFLKVRESNTTECDSKIIGTAVKNNLAIHSDLSYWIESRLNDTWKLERAVLGEVKSCTWPETHTLWGDGILESDLIIPVTLAGPRSNHNRRPGYKTQNQGPWDEGRVEIDFDYCPGTTVTLSESCGHRGPATRTTTESGKLITDWCCRSCTLPPLRYQTDSGCWYGMEIRPQRHDEKTLVQSQVNA 352
                                     3        13        23        33        43        53        63        73        83        93       103   ||  134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344        
                                                                                                                                           107|                                                                                                                                                                                                                               
                                                                                                                                            129                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeee....eeeeeeeeeee.........eeeee.hhhhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhhhhhhhhh....eeee...................eeee........hhh.ee...eeeeeee.....eeeeeee........hhhhheeeee..eeeee...eeeeeee...eeeeeeee........hhhhh......hhhhh..hhhhh........................eeeee......eeee..........ee..........eeee.......eeeee..eeee...eee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o6d B -24 xxxxxxFQSNADTGCAIDISRQELRCGSGVFIHNDVEAWMDRYKYYPETPQGLAKIIQKAHKEGVCGLRSVSRLEHQMWEAVKDELNTLLKENGVDLSVVVEKQEGMYKSAPKRLTATNNTFVVDGPETKECPTQNRAWNSLEVEDFGFGLTSTRMFLKVRESNTTECDSKIIGTAVKNNLAIHSDLSYWIESRLNDTWKLERAVLGEVKSCTWPETHTLWGDGILESDLIIPVTLAGPRSNHNRRPGYKTQNQGPWDEGRVEIDFDYCPGTTVTLSESCGHRGPATRTTTESGKLITDWCCRSCTLPPLRYQTDSGCWYGMEIRPQRHDEKTLVQSQVNA 352
                            ||||||| -1         9        19        29        39        49        59        69        79        89        99       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351 
                          -24-UNK||                                                                                                            107|                                                                                                                                                                                                                              
                           -23-UNK|                                                                                                             130                                                                                                                                                                                                                              
                            -22-UNK                                                                                                                                                                                                                                                                                                                                              
                             -21-UNK                                                                                                                                                                                                                                                                                                                                             
                              -20-UNK                                                                                                                                                                                                                                                                                                                                            
                               -19-UNK                                                                                                                                                                                                                                                                                                                                           
                                 -4
   Legend:   → Mismatch (orange background)
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    → 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 4O6D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O6D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O6D)

(-) Gene Ontology  (45, 90)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9Q6P4_WNV | Q9Q6P4: 2of6 3ixx
        U3N977_WNV | U3N977: 4o6c 4oie 4oii
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        Q9Q6P4_WNV | Q9Q6P4: 2oy0 3i50 3iyw 3j0b 3lkz 4o6c 4oie 4oii

(-) Related Entries Specified in the PDB File

4o6b 4o6c