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(-) Description

Title :  CRYSTAL STRUCTURE OF H1 HEMAGGLUTININ FROM A/CALIFORNIA/04/2009 IN COMPLEX WITH A NEUTRALIZING ANTIBODY 3E1
 
Authors :  W. Wang, T. Zhang, J. Ding
Date :  01 Jul 16  (Deposition) - 07 Dec 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  A,B,H,L  (3x)
Keywords :  Epitope, Fab, Complementarity Determining Region, Paratope, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Wang, X. Sun, Y. Li, J. Su, Z. Ling, T. Zhang, F. Wang, H. Zhang, H. Chen J. Ding, B. Sun
Human Antibody 3E1 Targets The Ha Stem Region Of H1N1 And H5N6 Influenza A Viruses
Nat Commun V. 7 13577 2016
PubMed-ID: 27910950  |  Reference-DOI: 10.1038/NCOMMS13577

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: A
    Engineered: YES
    Expression System: BACULOVIRUS EXPRESSION VECTOR PFASTBAC1-HM
    Expression System Plasmid: PFAST-HTB
    Expression System Strain: SF9
    Expression System Taxid: 274590
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 18-344
    Gene: HA
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 641501
    Strain: SWL A/CALIFORNIA/04/2009 H1N1
 
Molecule 2 - HEMAGGLUTININ
    Chains: B
    Engineered: YES
    Expression System: BACULOVIRUS EXPRESSION VECTOR PFASTBAC1-HM
    Expression System Plasmid: PFAST-HTB
    Expression System Strain: SF9
    Expression System Taxid: 274590
    Expression System Vector Type: PLASMID
    Fragment: NEUTRALIZING ANTIBODY 3E1
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 641501
    Strain: SWL A/CALIFORNIA/04/2009 H1N1
 
Molecule 3 - LIGHT CHAIN OF HUMAN NEUTRALIZING ANTIBODY 3E1
    Chains: L
    Engineered: YES
    Expression System: CLONING VECTOR ABVEC-HIGKAPPA
    Expression System Plasmid: ABVEC-HIGKAPPA2
    Expression System Taxid: 583343
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - HEAVY CHAIN OF HUMAN NEUTRALIZING ANTIBODY 3E1
    Chains: H
    Engineered: YES
    Expression System: CLONING VECTOR ABVEC-HIGG1
    Expression System Plasmid: ABVEC-HIGG1
    Expression System Taxid: 583342
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (3x): ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:74 , ASP A:96 , ASN A:97 , CYS A:100 , ARG A:231 , GLN L:147 , SER L:156binding site for Poly-Saccharide residues NAG A 401 through NAG A 402 bound to ASN A 97
2AC2SOFTWAREASP A:284 , ASN A:286binding site for Mono-Saccharide NAG A 403 bound to ASN A 286

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:14 -B:137
2A:52 -A:285
3A:65 -A:77
4A:100 -A:146
5A:289 -A:313
6B:144 -B:148
7H:22 -H:95
8H:148 -H:204
9L:23 -L:88
10L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Ser H:54 -Gly H:55
5Gly H:104 -Gly H:105
6Phe H:154 -Pro H:155
7Glu H:156 -Pro H:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GJS)

(-) Sequences/Alignments

Asymmetric 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:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhh.............eee...............hhhhhhhhhh.....eeee..hhhhhh..ee.....eeeee....ee....eee.ee.......eeeeee.....eeeeeeeeee..hhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeee......eee....eeeeee.eee..eee.....ee......ee...ee......eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gjs A  10 SDTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYNADTYVFVCSSRYSKKFKPEIAICPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNASGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPS 333
                                    19        29        39        49        59        69        79|       91       101       111       121       131       141       151       161       171       181       191       201||     212       222       232       242       252       262       273       283       293       303       313       323       333
                                                                                                79|                                                                                                                     202|                                                                271|                                                            
                                                                                                 82                                                                                                                      204                                                                 273                                                            


Chain B from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeee.....eeeehhhhhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gjs B   4 GAIAFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNRE 171
                               ||   14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       
                               7|                                                                                                                                                                  
                                9                                                                                                                                                                  


Chain H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee.......eeeeeee.....eeeeee......ee.......eeeeee....eeeeee...hhhhheeeeeeee.........eeee...eee..........eeeee...eeeeeeeeee.....eeee........eee...ee.....eeeeeeeee........eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gjs H   1 QVQLQESGPGLVKPSETLSLTCSVSGASISSYYWIWIRQPAKGLEWIGRFYTSGSPNYNPSLRSRVTMSVDTSKNQFSLKLTSVTAADTAVYYCAREEHITFGGVIVRYWGQGTLVTVSPASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGQTYICNVNHKPSNTKVDKKVEP 221
                                    10        20        30        40||      51        61        71        81        91       101       111       121       131  ||   149       159       169       179       189       200       210       220 
                                                                   41|                                                                                        134|                                                    198|                     
                                                                    43                                                                                         143                                                     200                     


Chain L from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh...eeeeeeeeee.....eeeee.......eeeee.........eeeeeeeee......eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gjs L   1 DIQMTQSPATLSASVGDRVSITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPSRFSGSGSGSEFTLTISSLQPDDFAIYYCQQYNSYPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVNALQSNSQESVTEQDSKDSTYSLSSTLTLDYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150|   || 162       172       185       195       205       
                                                                                                                                                                               150| 156|                    181|                           
                                                                                                                                                                                152  158                     185
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5GJS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

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    Ser L:7 - Pro L:8   [ RasMol ]  
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UniProtKB/TrEMBL
        C3W5S1_I09A0 | C3W5S1: 3al4 3lzg 3ube 3ubj 3ubn 3ubq 3uyw 3uyx 3ztn 4jtv 4jtx 4ju0 4m4y 5k9o

(-) Related Entries Specified in the PDB File

5gjt