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(-) Description

Title :  ANTIBODY HEMAGGLUTININ COMPLEXES
 
Authors :  B. W. Spiller, K. L. Winarski
Date :  20 Jan 15  (Deposition) - 15 Jul 15  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym. Unit :  A,B,C,D,H,L
Biol. Unit 1:  A,B,D  (1x)
Biol. Unit 2:  C,H,L  (1x)
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

(-) Compounds

Molecule 1 - H5.3 FAB 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 FAB 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 - HEMAGGLUTININ
    Chains: D, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 15-226
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Strain: A/VIETNAM/1203/2004(H5N1)

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDHL
Biological Unit 1 (1x): AB D  
Biological Unit 2 (1x):   C HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FUC-1Ligand/IonALPHA-L-FUCOSE
2NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (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:63binding site for Poly-Saccharide residues NAG L 301 through NAG L 303 bound to ASN L 18

(-) SS Bonds  (12, 12)

Asymmetric 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  (9, 9)

Asymmetric 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
5Tyr L:139 -Pro L:140
6Pro H:14 -Ser H:15
7Asp H:111 -Pro H:112
8Phe H:156 -Pro H:157
9Glu H:158 -Pro H:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XRC)

(-) 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:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....eeeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeeee..hhhhheeeeeeeee..eeee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhh....eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xrc 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:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeeee......eeeeee...eeeee........eeeee....eeeeeeeee.....eeee........eee...ee.....eeeeeeee..........eeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xrc B    1 QVQLQESGPGLVKPSGTVSLTCAVSGGSISSSYWWSWVRQPPGKGLEWIGEIYHSGNTNYNPSLKSRVTISVDKSKNLFSLKLSSVTAADTAVYYCARVALFDILTGGWFDPWGQGTLVTVSSASTKGPSVFPLAPSAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEL  223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |148       158       168       178       188       198       208       218     
                                                                                                                                                                  137|                                                                             
                                                                                                                                                                   146                                                                             


Chain C from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhhhh..........eee...........eee.hhhhhhhhhh...eeeeee..hhhhh.........eeeeee..eee....eee..........eeeeee.....eeeeeeeeee..hhhhhhhhh......eeeee..eeeee...............eeeeeeeee....eeeeee...eeee.eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xrc C   57 KPLILRDCSVAGWLLGNPMCDEEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSAYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGLSSRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVK  262
                                    66        76 ||     90      | 99       109       119      |127      |136       146       156       166       176       186       196       206       216       226       236       246       256      
                                                78|           96A                          125A|     133A                                                                                                                                 
                                                 83                                         125B                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               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..hhhhhhhhh......eeeee..eeeee...............eeeeeeeee....eeeeee...eeee.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xrc D   57 KPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSAYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGLSSRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVK  262
                                    66        76      | 85        95 |     104       114       124 ||    132 |     141       151       161       171       181       191       201       211       221       231       241       251       261 
                                                    82A            96A                          125A|     133A                                                                                                                                 
                                                                                                 125B                                                                                                                                          


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.......eeeeee....eeeeee...hhhhheeeeeeeeee......eeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xrc 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....eeeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeeee..hhhhheeeeeeeee..eeee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee..........eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xrc 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 4XRC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 34)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4xnm