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(-) Description

Title :  ANTIBODY HEMAGGLUTININ COMPLEXES
 
Authors :  B. W. Spiller, K. L. Winarski
Date :  15 Jan 15  (Deposition) - 15 Jul 15  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,H,L
Keywords :  Antibody, Hemagglutinin, Neutralization, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Winarski, N. J. Thornburg, Y. Yu, G. Sapparapu, J. E. Crowe, B. W. Spiller
Vaccine-Elicited Antibody That Neutralizes H5N1 Influenza And Variants Binds The Receptor Site And Polymorphic Sites.
Proc. Natl. Acad. Sci. Usa V. 112 9346 2015
PubMed-ID: 26170302  |  Reference-DOI: 10.1073/PNAS.1502762112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - H5.3 LIGHT CHAIN
    Chains: A, L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - H5.3 HEAVY CHAIN
    Chains: B, H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - INFLUENZA H5 HA HEAD DOMAIN VIETNAM RDT MUTATIONS
    Chains: D, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 74-285
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Strain: A/VIETNAM/1203/2004(H5N1)

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDHL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR L:16 , ASN L:18 , SER L:63 , THR L:70 , HOH L:404binding site for Poly-Saccharide residues NAG L 301 through NAG L 303 bound to ASN L 18

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:21 -A:86
2A:133 -A:192
3B:22 -B:96
4B:150 -B:206
5C:64 -C:76
6C:97 -C:139
7D:64 -D:76
8D:97 -D:139
9H:22 -H:96
10H:150 -H:206
11L:21 -L:86
12L:133 -L:192

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Tyr A:139 -Pro A:140
2Asp B:111 -Pro B:112
3Phe B:156 -Pro B:157
4Glu B:158 -Pro B:159
5Val D:261 -Lys D:262
6Tyr L:139 -Pro L:140
7Asp H:111 -Pro H:112
8Phe H:156 -Pro H:157
9Glu H:158 -Pro H:159
10Lys C:90 -Ala C:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XNQ)

(-) 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:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xnq A    1 YELTQPPSVSVSPGQTVNITCSGDTLGDKYVCWYQQKPGQSPVLVIYQDTKRPSGIPERFSGSNSGDTATLTVSGTQAMDEADYYCQAWDSSSFVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee......eeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeeeeee......eeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xnq B    1 QVQLQESGPGLVKPSGTVSLTCAVSGGSISSSYWWSWVRQPPGKGLEWIGEIYHSGNTNYNPSLKSRVTISVDKSKNLFSLKLSSVTAADTAVYYCARVALFDILTGGWFDPWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEL  223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |146       156       166       176       186       196       206       216       
                                                                                                                                                                  137|                                                                               
                                                                                                                                                                   144                                                                               


Chain C from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhhhh.....ee..eee...........eee.hhhhhhhhhh...eeeeee..hhhhh.........eeeeee..eee....eee..........eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee.......eeeeeeeee....eeeeee...eeee.eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xnq C   57 KPLILRDCSVAGWLLGNPMCPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKDSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIASGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVK  262
                                    66        76|       91     | 100       110       120     ||128     | 137       147       157       167       177       187       197       207       217||     235       245       255       
                                              76|            96A                          125A|     133A                                                                                  218|                                   
                                              82A                                          125B                                                                                            227                                   


Chain D from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhhhh...............eee...........eee.hhhhhhhhhhh..eeeeee..hhhhh.........eeeeee..eee....eee..........eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeeee..eeeee......eeeeeeeee....eeeeee...eeee.eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xnq D   57 KPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKDSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRISGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVK  262
                                    66        76      | 85        95|      104       114       124 ||    132 |     141       151       161       171       181       191       201       211     ||230       240       250       260  
                                                    82A           96A                           125A|     133A                                                                                 217|                                   
                                                                                                 125B                                                                                           227                                   


Chain H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee......eeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeeeeee......eeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xnq H    1 QVQLQESGPGLVKPSGTVSLTCAVSGGSISSSYWWSWVRQPPGKGLEWIGEIYHSGNTNYNPSLKSRVTISVDKSKNLFSLKLSSVTAADTAVYYCARVALFDILTGGWFDPWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEL  223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |146       156       166       176       186       196       206       216       
                                                                                                                                                                  137|                                                                               
                                                                                                                                                                   144                                                                               


Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xnq L    1 YELTQPPSVSVSPGQTVNITCSGDTLGDKYVCWYQQKPGQSPVLVIYQDTKRPSGIPERFSGSNSGDTATLTVSGTQAMDEADYYCQAWDSSSFVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 4XNQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H8PCX0_9INFA | H8PCX0: 4xnm
        Q6DQ33_9INFA | Q6DQ33: 3fku 4mhh
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        Q6DQ33_9INFA | Q6DQ33: 3gbm 4fqi 4kdm 4kdn 4kdo 4n5y 4n5z 4xnm 4xrc 5a3i

(-) Related Entries Specified in the PDB File

4xnm 4xrc