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(-) Description

Title :  CRYSTAL STRUCTURE OF MULTIDONOR HV1-18+HD3-9 CLASS BROADLY NEUTRALIZING INFLUENZA A ANTIBODY 31.B.09 IN COMPLEX WITH HEMAGGLUTININ H1 A/CALIFORNIA/04/2009
 
Authors :  M. G. Joyce, P. V. Thomas, A. K. Wheatley, A. B. Mcdermott, J. R. Mascola,
Date :  01 Jun 16  (Deposition) - 28 Dec 16  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.39
Chains :  Asym./Biol. Unit :  A,B,F,H,I,L
Keywords :  Hv1-18, Multidonor, H5, Universal Influenza Vaccine, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. G. Joyce, A. K. Wheatley, P. V. Thomas, G. Y. Chuang, C. Soto, R. T. Bailer, A. Druz, I. S. Georgiev, R. A. Gillespie, M. Kanekiyo, W. P. Kong, K. Leung, S. N. Narpala, M. S. Prabhakaran, E. S. Yang, B. Zhang, Y. Zhang, M. Asokan, J. C. Boyington, T. Bylund, S. Darko, C. R. Lees, A. Ransier, C. H. Shen, L. Wang, J. R. Whittle, X. Wu, H. M. Yassine, C. Santos, Y. Matsuoka, Y. Tsybovsky, U. Baxa, J. C. Mullikin, K. Subbarao, D. C. Douek, B. S. Graham, R. A. Koup, J. E. Ledgerwood, M. Roederer, L. Shapiro, P. D. Kwong, J. R. Mascola, A. B. Mcdermott
Vaccine-Induced Antibodies That Neutralize Group 1 And Grou 2 Influenza A Viruses.
Cell V. 166 609 2016
PubMed-ID: 27453470  |  Reference-DOI: 10.1016/J.CELL.2016.06.043

(-) Compounds

Molecule 1 - 31.B.09 HEAVY FV
    Chains: A, H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 31.B.09 LIGHT FV
    Chains: B, L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - HEMAGGLUTININ
    Chains: F, I
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS (STRAIN SWL A/CALIFORNIA/04/2009 H1N1)
    Organism Taxid: 641501
    Strain: SWL A/CALIFORNIA/04/2009 H1N1

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABFHIL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN I:33binding site for Poly-Saccharide residues NAG I 601 through BMA I 603 bound to ASN I 33

(-) SS Bonds  (21, 21)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:96
2A:149 -A:205
3A:225 -B:219
4B:23 -B:93
5B:139 -B:199
6F:14 -F:466
7F:52 -F:277
8F:64 -F:76
9F:97 -F:139
10F:281 -F:305
11F:473 -F:477
12H:22 -H:96
13H:149 -H:205
14H:225 -L:219
15I:14 -I:466
16I:52 -I:277
17I:64 -I:76
18I:97 -I:139
19I:473 -I:477
20L:23 -L:93
21L:139 -L:199

(-) Cis Peptide Bonds  (19, 19)

Asymmetric/Biological Unit
No.Residues
1Gly A:26 -Tyr A:27
2Tyr A:54 -Asn A:55
3Phe A:155 -Pro A:156
4Glu A:157 -Pro A:158
5Ser B:7 -Pro B:8
6Tyr B:145 -Pro B:146
7Leu F:51 -Cys F:52
8Leu F:79 -Ser F:80
9Pro F:284 -Lys F:285
10Ala F:287 -Ile F:288
11Ile F:288 -Asn F:289
12Tyr H:27 -Ser H:28
13Phe H:155 -Pro H:156
14Glu H:157 -Pro H:158
15Leu I:79 -Ser I:80
16Lys I:496 -Leu I:497
17Ser L:7 -Pro L:8
18Asp L:75 -Phe L:76
19Tyr L:145 -Pro L:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K9O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K9O)

(-) Exons   (0, 0)

(no "Exon" information available for 5K9O)

(-) 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:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...ee......eeeeee..........eeeeee.....eeeeeee.......ee.hhhh...eeeee....eeeeee...hhhhheeeeeee.................eeee.....eeeee...........eeeeeeeeee.....eeee........eee...ee.....eeeeeeeeehhhhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5k9o A    1 QVQLVQSGAEVKKPGASVKVSCKASGYSFSSYGISWVRQAPGQGLEWMGWISAYNGNTNYAQKLQGRVTMTTDTSTSTAYMELRSLRSDDTAVFYCARDRPHILTGFDFDYWGQGTLVTSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  225
                                    10        20        30        40        50        60        70        80        90       100       110       124       134       144       154       164       174       184       194       204       214       224 
                                                                                                                                                119|                                                                                                     
                                                                                                                                                 124                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eee......eeeeee.................ee.........ee...ee.......eeee....eeeeee........eee...............eeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5k9o B    5 TQSPVSLPVTLGQPASISCRSSQGLVYIDGNTYLNWFQQRPGQSPRRLIYNVFTRDSGVPDRFSGSGSGTDFTLKITTVEAEDVGVYYCMQGTHWPYTFGQGTKVEITVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC  219
                                    14        24        34        44        54        64        74        84        94       104      |116       126       136       146       156       166       176       186       196       206       216   
                                                                                                                                    111|                                                                                                         
                                                                                                                                     114                                                                                                         


Chain F from PDB  Type:PROTEIN  Length:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......ee.......ee...eee........................hhhhhhhh...............eee...............hhhhhhhhhhheeeeeeee..hhhhhh.........eeeee....ee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee........................ee...........ee......eee............................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeee....hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5k9o F   11 DTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKY  491
                                    20        30        40        50     |  59        69        79    |   88  |     97       107      116A||     124      133A       143       153       163       173       183       193       203       213       223       233       243       253       263   |   272       282       292       302       312       322 ||    337       347       357       367       377       387    || 414       424       434       444       454       464       474       484       
                                                                       55A                          83A     90A                       116A||              133A                                                                                                                                  266A                                                       324|                                                           392|                                                                                 
                                                                                                                                       116B|                                                                                                                                                                                                                330                                                            410                                                                                 
                                                                                                                                        116C                                                                                                                                                                                                                                                                                                                                                                   


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...ee......eeeeee..........eeeeee.....eeeeeee.......ee........eeeee....eeeeee.........eeeeee.................eeee.....eeeee...........eeeeeeeeee....eeeee........eee...ee.....eeeeeeeeehhhhh.....eeeeee.hhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5k9o H    1 QVQLVQSGAEVKKPGASVKVSCKASGYSFSSYGISWVRQAPGQGLEWMGWISAYNGNTNYAQKLQGRVTMTTDTSTSTAYMELRSLRSDDTAVFYCARDRPHILTGFDFDYWGQGTLVTSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  225
                                    10        20        30        40        50        60        70        80        90       100       110       124       134       144       154       164       174       184       194       204       214       224 
                                                                                                                                                119|                                                                                                     
                                                                                                                                                 124                                                                                                     


Chain I from PDB  Type:PROTEIN  Length:466
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......ee.......ee...eee..................ee....hhhhhhhh...............eee...............hhhhhhhhhhheeeeeeee.................eeeee....ee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee........................ee...........ee......eee...........................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeee....hhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5k9o I   11 DTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPSIQSRGGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKL  497
                                    20        30        40        50     |  59        69        79    |   88  |     97       107      116A||     124      133A       143       153       163       173       183       193       203       213       223       233       243       253       263   |   272       282       292       302       312       322       338       348       358       368       378       388  ||   421       431       441       451       461       471       481       491      
                                                                       55A                          83A     90A                       116A||              133A                                                                                                                                  266A                                                             330|                                                   391|                                                                                  
                                                                                                                                       116B|                                                                                                                                                                                                                      337                                                    415                                                                                  
                                                                                                                                        116C                                                                                                                                                                                                                                                                                                                                                                  


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee......eeeeee................eee.......................eeeee....eeeee........eeee...............eee......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5k9o L    1 DVVMTQSPVSLPVTLGQPASISCRSSQGLVYIDGNTYLNWFQQRPGQSPRRLIYNVFTRDSGVPDRFSGSGSGTDFTLKITTVEAEDVGVYYCMQGTHWPYTFGQGTKVEITVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC  219
                                    10        20        30        40        50        60        70        80        90       100       110||     122       132       142       152       162       172       182       192       202       212       
                                                                                                                                        111|                                                                                                         
                                                                                                                                         114
   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 5K9O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K9O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K9O)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        C3W5S1_I09A0 | C3W5S1: 3al4 3lzg 3ube 3ubj 3ubn 3ubq 3uyw 3uyx 3ztn 4jtv 4jtx 4ju0 4m4y 5gjs

(-) Related Entries Specified in the PDB File

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