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(-) Description

Title :  WEST NILE VIRUS NS1 IN COMPLEX WITH NEUTRALIZING 22NS1 ANTIBODY FAB
 
Authors :  M. A. Edeling, D. H. Fremont, Center For Structural Genomics Of In Diseases (Csgid)
Date :  19 Jan 14  (Deposition) - 05 Mar 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,H,I,L,M
Keywords :  West Nile Virus, Antibody, Fab, Neutralizing, Flavivirus, Non- Structural Protein, Ns1, Viral Protein-Immune System Complex, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Edeling, M. S. Diamond, D. H. Fremont
Structural Basis Of Flavivirus Ns1 Assembly And Antibody Recognition.
Proc. Natl. Acad. Sci. Usa V. 111 4285 2014
PubMed-ID: 24594604  |  Reference-DOI: 10.1073/PNAS.1322036111

(-) Compounds

Molecule 1 - NON-STRUCTURAL PROTEIN NS1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21(A)+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 963-1143
    Organism Common: WNV
    Organism Scientific: WEST NILE VIRUS
    Organism Taxid: 11082
 
Molecule 2 - LIGHT CHAIN OF FAB FRAGMENT OF 22NS1 ANTIBODY
    Chains: L, M
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - HEAVY CHAIN OF FAB FRAGMENT OF 22NS1 ANTIBODY
    Chains: H, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABHILM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4OII)

(-) Sites  (0, 0)

(no "Site" information available for 4OII)

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:179 -A:223
2A:280 -A:329
3A:291 -A:312
4A:313 -A:316
5B:179 -B:223
6B:280 -B:329
7B:291 -B:312
8B:313 -B:316
9H:22 -H:92
10H:142 -H:208
11I:22 -I:92
12I:142 -I:208
13L:23 -L:88
14L:134 -L:194
15M:23 -M:88
16M:134 -M:194

(-) Cis Peptide Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1Leu A:318 -Pro A:319
2Leu B:318 -Pro B:319
3Ser L:7 -Pro L:8
4Gln L:40 -Gly L:41
5Thr L:94 -Pro L:95
6Tyr L:140 -Pro L:141
7Phe H:148 -Pro H:149
8Glu H:150 -Pro H:151
9Trp H:199 -Pro H:200
10Ser M:7 -Pro M:8
11Gln M:40 -Gly M:41
12Thr M:94 -Pro M:95
13Tyr M:140 -Pro M:141
14Phe I:148 -Pro I:149
15Glu I:150 -Pro I:151
16Trp I:199 -Pro I:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OII)

(-) 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:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee..eeeee...eeeeeee...eeeeeeee........hhhhh......hhhhh..hhhhh........................eeeee......eeee......................eeee.......eeeee..eeee....ee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oii A 176 TTECDSKIIGTAVKNNLAIHSDLSYWIESRLNDTWKLERAVLGEVKSCTWPETHTLWGDGILESDLIIPVTLAGPRSNHNRRPGYKTQNQGPWDEGRVEIDFDYCPGTTVTLSESCGHRGPATRTTTESGKLITDWCCRSCTLPPLRYQTDSGCWYGMEIRPQRHDEKTLVQSQVNA 352
                                   185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       


Chain B from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee..eeeee...eeeeeee...eeeeeeee........hhhhh......hhhhh..hhhhh........................eeeee......eeee......................eeee.......eeeee..eeee....ee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oii B 176 TTECDSKIIGTAVKNNLAIHSDLSYWIESRLNDTWKLERAVLGEVKSCTWPETHTLWGDGILESDLIIPVTLAGPRSNHNRRPGYKTQNQGPWDEGRVEIDFDYCPGTTVTLSESCGHRGPATRTTTESGKLITDWCCRSCTLPPLRYQTDSGCWYGMEIRPQRHDEKTLVQSQVNA 352
                                   185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       


Chain H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.......ee...eeeee........eeeee..........eeeeeeeeeee.....eeee........eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oii H   1 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKLRPGQGFEWIGDINPNNGGPSYNEKFKRKATLTVDTSSSTAYMQLSSLTSEDSAVYYCTIDDGYRFGYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 228
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126   ||  138       148     ||163     ||174     ||186       196| ||   209       219   ||  
                                                                              52A                            82A||                                             130|                  154|||    169|      180|          196| || 206|            223|  
                                                                                                              82B|                                              133                   156||     171       183           198 ||  208             226  
                                                                                                               82C                                                                     157|                               200|                       
                                                                                                                                                                                        162                                202                       


Chain I from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.......ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oii I   1 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKLRPGQGFEWIGDINPNNGGPSYNEKFKRKATLTVDTSSSTAYMQLSSLTSEDSAVYYCTIDDGYRFGYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 228
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126   ||  138       148     ||163     ||174     ||186       196| ||   209       219   ||  
                                                                              52A                            82A||                                             130|                  154|||    169|      180|          196| || 206|            223|  
                                                                                                              82B|                                              133                   156||     171       183           198 ||  208             226  
                                                                                                               82C                                                                     157|                               200|                       
                                                                                                                                                                                        162                                202                       


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oii L   1 DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSASGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain M from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oii M   1 DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSASGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 4OII)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 90)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Cis Peptide Bonds
    Gln L:40 - Gly L:41   [ RasMol ]  
    Gln M:40 - Gly M:41   [ RasMol ]  
    Glu H:150 - Pro H:151   [ RasMol ]  
    Glu I:150 - Pro I:151   [ RasMol ]  
    Leu A:318 - Pro A:319   [ RasMol ]  
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    Tyr M:140 - Pro M:141   [ RasMol ]  
 

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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 4o6d 4oie
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        Q9Q6P4_WNV | Q9Q6P4: 2oy0 3i50 3iyw 3j0b 3lkz 4o6c 4o6d 4oie

(-) Related Entries Specified in the PDB File

4oie WEST NILE VIRUS NS1
4oig DENGUE VIRUS NS1 RELATED ID: CSGID-IDP93954 RELATED DB: TARGETTRACK