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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB CR9114 IN COMPLEX WITH A H5N1 INFLUENZA VIRUS HEMAGGLUTININ
 
Authors :  C. Dreyfus, I. A. Wilson
Date :  25 Jun 12  (Deposition) - 22 Aug 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  A,B,H,L  (3x)
Keywords :  Neutralizing Antibodies, Antibody Affinity, Antigens, Epitopes, Glycosylation, Hemagglutinin Glycoproteins, Immunoglobulin Fab Fragments, H5N1 Subtype, Influenza Vaccines, Avian Flu, Envelope Protein, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Dreyfus, N. S. Laursen, T. Kwaks, D. Zuijdgeest, R. Khayat, D. C. Ekiert, J. H. Lee, Z. Metlagel, M. V. Bujny, M. Jongeneelen, R. Van Der Vlugt, M. Lamrani, H. J. Korse, E. Geelen, Sahin, M. Sieuwerts, J. P. Brakenhoff, R. Vogels, O. T. Li, L. L. Poon, M. Peiris, W. Koudstaal, A. B. Ward, I. A. Wilson, J. Goudsmit, R. H. Friesen
Highly Conserved Protective Epitopes On Influenza B Viruses
Science V. 337 1343 2012
PubMed-ID: 22878502  |  Reference-DOI: 10.1126/SCIENCE.1222908

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 17-346
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 284218
    Strain: A/VIET NAM/1203/2004(H5N1)
    Synonym: HEMAGGLUTININ RECEPTOR BINDING SUBUNIT HA1
 
Molecule 2 - HEMAGGLUTININ HA2
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 347-520
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 284218
    Strain: A/VIET NAM/1203/2004(H5N1)
    Synonym: HEMAGGLUTININ MEMBRANE FUSION SUBUNIT HA2
 
Molecule 3 - ANTIBODY CR9114 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - ANTIBODY CR9114 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: FAB LAMBDA
    Organism Common: HUMAN
    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  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 51)
No.NameCountTypeFull Name
1EDO33Ligand/Ion1,2-ETHANEDIOL
2GOL3Ligand/IonGLYCEROL
3NAG15Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:26 , ASP A:27 , ARG A:313 , LEU A:314 , VAL A:315 , HOH A:522 , VAL B:100 , ASN B:104BINDING SITE FOR RESIDUE EDO A 401
02AC2SOFTWAREASP A:96 , ASP A:101 , PHE A:102 , TYR A:105 , HOH A:952BINDING SITE FOR RESIDUE EDO A 402
03AC3SOFTWAREGLY A:100 , ASP A:101 , HIS A:184 , ASN A:210 , ARG A:216 , ARG A:229 , GLU A:231 , HOH A:857BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWARETRP A:69 , PHE A:79 , ILE A:80 , ASN A:81 , VAL A:82 , LYS A:120 , TYR A:258 , HOH A:514 , HOH A:518BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWAREASN A:21 , GLN B:15BINDING SITE FOR RESIDUE NAG A 405
06AC6SOFTWAREGLN A:122 , HOH A:564 , PRO H:14 , THR H:83 , SER H:84 , VAL H:111 , SER H:113BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWAREASN A:169 , ASN A:240 , NAG A:408 , HOH A:782 , HOH A:894BINDING SITE FOR RESIDUE NAG A 407
08AC8SOFTWAREASN A:240 , NAG A:407BINDING SITE FOR RESIDUE NAG A 408
09AC9SOFTWAREASN A:33 , HOH A:899BINDING SITE FOR RESIDUE NAG A 409
10BC1SOFTWAREHOH A:504 , TRP B:14 , EDO B:202 , HOH B:479BINDING SITE FOR RESIDUE GOL B 201
11BC2SOFTWARETRP B:14 , TYR B:34 , GOL B:201BINDING SITE FOR RESIDUE EDO B 202
12BC3SOFTWAREEDO B:204BINDING SITE FOR RESIDUE EDO B 203
13BC4SOFTWAREGLN B:42 , ASP B:46 , EDO B:203 , TYR H:32 , GLY H:96BINDING SITE FOR RESIDUE EDO B 204
14BC5SOFTWAREASN B:50 , HOH B:450 , ASN H:31BINDING SITE FOR RESIDUE EDO B 205
15BC6SOFTWAREALA B:36 , ASP B:37 , LYS B:38 , GLU B:39 , ARG B:153BINDING SITE FOR RESIDUE EDO B 206
16BC7SOFTWAREGLU B:147 , GLU B:150 , ASN B:154 , THR B:156BINDING SITE FOR RESIDUE NAG B 207
17BC8SOFTWAREASP B:19 , LYS B:38 , HOH B:537 , ASN H:97 , TYR H:98 , TYR H:99 , TYR H:100A , HOH H:417 , HOH H:569 , HOH H:570BINDING SITE FOR RESIDUE EDO H 301

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:14 -B:137
2A:52 -A:277
3A:64 -A:76
4A:97 -A:139
5A:281 -A:305
6B:144 -B:148
7H:22 -H:92
8H:140 -H:196
9L:23 -L:88
10L:134 -L:193

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FQI)

(-) 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:324
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4fqia_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhhh.eeeeeeee..hhhhh.........eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeeee....eee....eeeeee.eee..eee.....ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4fqi A    8 DPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP  324
                                    17        27        37        47        56        66        76       |85        95 |     104       114       124 ||    132 |     141       151       161       171       181       191       201       211       221       231       241       251      260A       270       280       290       300       310       320    
                                                                          55A                          83A           96A                          125A|     133A                                                                                                                            260A                                                                
                                                                                                                                                   125B                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                 
               SCOP domains d4fqib_ B: Influenza hemagglutinin (stalk)                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fqi B    1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSG  176
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      


Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.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
                4fqi H    1 QVQLVQSGAEVKKPGSSVKVSCKSSGGTSNNYAISWVRQAPGQGLDWMGGISPIFGSTAYAQKFQGRVTISADIFSNTAYMELNSLTSEDTAVYFCARHGNYYYYSGMDVWGQGTTVTVSSASTKGPSVFPLAPGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122   ||  138       148       158       168       178       188       198       208     
                                                                              52A                            82A||               100A|||                       126|                                                                                
                                                                                                              82B|                100B||                        133                                                                                
                                                                                                               82C                 100C|                                                                                                           
                                                                                                                                    100D                                                                                                           


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains d4fqil1 L:2-107 automated matches                                                                             d4fqil2 L:108-208 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..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fqi L    2 SALTQPPAVSGTPGQRVTISCSGSDSNIGRRSVNWYQQFPGTAPKLLIYSNDQRPSVVPDRFSGSKSGTSASLAISGLQSEDEAEYYCAAWDDSLKGAVFGGGTQLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                   |12        22     || 30        40        50        60        70        80        90     || 98       107       117       127       137       147       157       167       177       187       197       207 
                                   9|              27A|                                                                  95A|        106A                                                                                                      
                                   11               27B                                                                   95B
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (4, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4fqi
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q6DQ33_9INFA | Q6DQ33: 3fku 4mhh
UniProtKB/TrEMBL
        Q6DQ33_9INFA | Q6DQ33: 3gbm 4kdm 4kdn 4kdo 4n5y 4n5z 4xnm 4xnq 4xrc 5a3i

(-) Related Entries Specified in the PDB File

4fnk 4fqh 4fqj 4fqk 4fql 4fqm 4fqv 4fqy