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(-) Description

Title :  CRYSTAL STRUCTURE OF INFLUENZA A VIRUS H5 HEMAGGLUTININ GLOBULAR HEAD IN COMPLEX WITH THE FAB OF ANTIBODY 65C6
 
Authors :  J. Sun, T. Zuo, G. Wang, P. Zhou, L. Zhang, X. Wang
Date :  19 Sep 15  (Deposition) - 16 Dec 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Influenza Virus, Antibody, Complex, Neutralize, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Zuo, J. Sun, G. Wang, L. Jiang, Y. Zuo, D. Li, X. Shi, X. Liu, S. Fan, H. Ren, H. Hu, L. Sun, B. Zhou, M. Liang, P. Zhou, X. Wang, L. Zhang
Comprehensive Analysis Of Antibody Recognition In Convalescent Humans From Highly Pathogenic Avian Influenza H5N1 Infection
Nat Commun V. 6 8855 2015
PubMed-ID: 26635249  |  Reference-DOI: 10.1038/NCOMMS9855

(-) Compounds

Molecule 1 - 65C6 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293T
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 65C6 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293T
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - HEMAGGLUTININ
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS (A/ANHUI/1/2005(H5N1))
    Organism Taxid: 370810
    Strain: A/ANHUI/1/2005(H5N1)

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:154binding site for Mono-Saccharide NAG A 301 bound to ASN A 154
2AC2SOFTWAREASN A:165 , ASN A:236binding site for Mono-Saccharide NAG A 302 bound to ASN A 165

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:55 -A:67
2A:90 -A:135
3H:22 -H:96
4H:154 -H:210
5L:23 -L:88
6L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ser H:29 -Thr H:30
2Ser H:126 -Ser H:127
3Phe H:160 -Pro H:161
4Glu H:162 -Pro H:163
5Ser L:7 -Pro L:8
6Trp L:94 -Pro L:95
7Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DUM)

(-) 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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh......................hhhhhhhhh.......eee..hhhhh.........eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dum A  49 PLILRDCSVAGWLLGNPMCIVEKANPANDLCYPGNFNDYEELKHLLSRINHFEKIQIIPKSSWSDHEASSGVSSACPYQGTPSFFRNVVWLIKKNNTYPTIKRSYNNTNQEDLLILWGIHHSNDAAEQTKLYQNPTTYISVGTSTLNQRLVPKIATRSKVNGQSGRMDFFWTILKPNDAINFESNGNFIAPEYAYKI 256
                                    58        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       
                                             67|                                                                                                                                                                                 
                                              79                                                                                                                                                                                 


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eee.....eeeeee........eeeeeeee......eeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeeee..eee...ee.....ee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dum H   2 VQLVQSGAEVKKPGESLRISCKGFAYSSTYFWISWVRQMPGKGLEWMGRIDPTDSYINYSPSFQGHVTISVDRSISTVYLQWSSLKASDTAMYYCAYHRRGHFYGSGSAWDWFESWGQGTLVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVESA 228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       149       159       169       179       189       199       209       219         
                                                                                                                                                                    140|                                                                               
                                                                                                                                                                     149                                                                               


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee....eeeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeeee..hhhhh.eeeeee......ee....eeee.......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeee........eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dum L   2 IVLTQSPLTLSVSPGERATLSCRASQSVSSNLAWYQQMPGQAPRLLIYGASTRATGIPARLSGSASGTEFTLTISSLQSEDFAVYYCQQYNNWPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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  (0, 0)

(no "SCOP Domain" information available for 5DUM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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UniProtKB/TrEMBL
        Q1WDM0_9INFA | Q1WDM0: 3mgt 5dup 5dur 5dut

(-) Related Entries Specified in the PDB File

5dup 5dur 5dut