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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF THE HUMAN NEUTRALIZING ANTI-WEST NILE VIRUS MAB CR4354
 
Authors :  B. Kaufmann, M. G. Rossmann
Date :  29 May 10  (Deposition) - 24 Nov 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Fab Fragment, Human Neutralizing Antibody, Mab Cr4354, Immune System, Anti-West Nile Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Kaufmann, M. R. Vogt, J. Goudsmit, H. A. Holdaway, A. A. Aksyuk, P. R. Chipman, R. J. Kuhn, M. S. Diamond, M. G. Rossmann
Neutralization Of West Nile Virus By Cross-Linking Of Its Surface Proteins With Fab Fragments Of The Human Monoclonal Antibody Cr4354.
Proc. Natl. Acad. Sci. Usa V. 107 18950 2010
PubMed-ID: 20956322  |  Reference-DOI: 10.1073/PNAS.1011036107

(-) Compounds

Molecule 1 - FAB FRAGMENT OF MAB CR4354, HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Strain: HUMAN EMBRYONIC KIDNEY 293 CELL LINE (HEK293T)
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB FRAGMENT OF MAB CR4354, LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Strain: HUMAN EMBRYONIC KIDNEY 293 CELL LINE (HEK293T)
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 3N9G)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:150 -H:206
3H:226 -L:219
4L:22 -L:89
5L:142 -L:201

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe H:156 -Pro H:157
2Glu H:158 -Pro H:159
3Tyr L:148 -Pro L:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N9G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N9G)

(-) Exons   (0, 0)

(no "Exon" information available for 3N9G)

(-) 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 H from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..........eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9g H   1 xVQLVQSGAEVRKPGASTKVSCKASGYTFTHYYMHWVRQAPGQGLEWMGIINPSGGSTTYAQKLQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDWGSNYVWGSYPKYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH 230
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
                            |                                                                                                                                                                                                                                     
                            1-PCA                                                                                                                                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains d3n9gl1 L:1-111 automated matches                                                                              d3n9gl2 L:112-220 automated matches                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeee............eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9g L   1 QSVLTQPSSVSGTPGQRVTISCSGSSSNIGSNTVNWYQQLPGTAPKLLIYGNNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGPVFGGGTKLTVLGAAAGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   Legend:   → Mismatch (orange background)
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  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N9G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3N9G)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3N9G)

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  Cis Peptide Bonds
    Glu H:158 - Pro H:159   [ RasMol ]  
    Phe H:156 - Pro H:157   [ RasMol ]  
    Tyr L:148 - Pro L:149   [ RasMol ]  
 

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 Related Entries

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(-) Related Entries Specified in the PDB File

5190 CRYO-ELECTRON MICROSCOPIC DENSITY VOLUME OF WEST NILE VIRUS COMPLEXED WITH CR4354 FAB FRAGMENTS