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(-) Description

Title :  CRYSTAL STRUCTURE OF HEMAGGLUTININ FROM TAIWAN (2013) H6N1 INFLUENZA VIRUS
 
Authors :  N. Tzarum, X. Zhu, I. A. Wilson
Date :  11 Jan 15  (Deposition) - 01 Apr 15  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  E,F  (1x)
Keywords :  Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Tzarum, R. P. De Vries, X. Zhu, W. Yu, R. Mcbride, J. C. Paulson, I. A. Wilson
Structure And Receptor Binding Of The Hemagglutinin From A Human H6N1 Influenza Virus.
Cell Host Microbe V. 17 369 2015
PubMed-ID: 25766295  |  Reference-DOI: 10.1016/J.CHOM.2015.02.005

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1 CHAIN
    Chains: A, C, E
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Expression System Vector: PFASTBAC-HT
    Expression System Vector Type: BACULOVIRUS
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 119212
    Strain: A/TAIWAN/2/2013 (H6N1)
 
Molecule 2 - HEMAGGLUTININ HA2 CHAIN
    Chains: B, D, F
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Expression System Vector: PFASTBAC-HT
    Expression System Vector Type: BACULOVIRUS
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 119212
    Strain: A/TAIWAN/2/2013 (H6N1)

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABCDEF
Biological Unit 2 (1x): AB    
Biological Unit 3 (1x):   CD  
Biological Unit 4 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:25 , ASP A:27 , ASN A:33binding site for Mono-Saccharide NAG A 401 bound to ASN A 33
2AC2SOFTWAREASN A:169 , THR A:242binding site for Mono-Saccharide NAG A 402 bound to ASN A 169
3AC3SOFTWAREGLU D:147 , GLU D:150 , ASN D:154binding site for Mono-Saccharide NAG D 201 bound to ASN D 154
4AC4SOFTWAREASN E:21binding site for Mono-Saccharide NAG E 401 bound to ASN E 21
5AC5SOFTWAREASN E:169 , THR E:171 , THR E:242binding site for Mono-Saccharide NAG E 402 bound to ASN E 169
6AC6SOFTWAREGLU C:122 , GLU F:147 , SER F:151 , ASN F:154binding site for Mono-Saccharide NAG F 201 bound to ASN F 154

(-) SS Bonds  (17, 17)

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
7C:14 -D:137
8C:52 -C:277
9C:64 -C:76
10C:97 -C:139
11C:281 -C:305
12D:144 -D:148
13E:14 -F:137
14E:52 -E:277
15E:97 -E:139
16E:281 -E:305
17F:144 -F:148

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala C:159 -Thr C:160
2Ala E:159 -Thr E:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XKD)

(-) 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:330
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.......ee.......ee...eee.ee......eee......ee....hhhhhhhhhhhhhhhh..ee...eee...........eee.hhhhhhhhhhheeeeeeee..hhhhh.........................eee...........eeeeee......eeeeeeeee..hhhhhhhhh......eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee......eee....eeeee..eee..eee.....ee.....eee...ee......eee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4xkd A    9 PGDKICIGYHANNSTTQVDTLLEKNVTVTHSVELLENQKEKRFCKIMNKAPLDLKDCTIEGWILGNPKCDLLLGDQSWSYIVERPNAQNGICYPGVLNELEELKAFIGSGERVERFEMFPKSTWAGVDTSRGVTNACPSYTIDSSFYRNLVWIVKTDSATYPVIKGTYNNTGTQPILYFWGVHHPLDTTVQDNLYGSGDKYVRMGTESMNFAKSPEIAARPAVNGQRSRIDYYWSVLRPGETLNVESNGNLIAPWYAYKFVSTNKKGAVFKSDLPIENCDATCQTITGVLRTNKTFQNVSPLWIGECPKYVKSESLRLATGLRNVPQIAT  328
                                    18        28        38        48       |57        67        77   |    86        96|      105       115       125||     132       142  |    151      |160       170       180       190       200       210       220       230       240       250       260   ||  268       278       288       298       308       318       328
                                                                         55A                       80A              96A                          125A|  130A           144A          157A                                                                                                       263A|                                                                 
                                                                                                                                                  125B                                                                                                                                           263B                                                                 


Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xkd B    1 GIFGAIAGFIEGGWTGMIDGWYGYHHENSQGSGYAADRESTQKAIDGITNKVNSIINKMNTQFEAVDHEFSNLERRIGNLNKRMEDGFLDVWTYNAELLVLLENERTLDLHDANVKNLYEKVKSQLRDNANDLGNGCFEFWHKCDNECMESVKNGTYDYPKYQKESKLNRQG  172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  


Chain C from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhh.hhhhhhhh..ee...eee...........eee.hhhhhhhhhhh..eeeeee..hhhhh..ee.....................eee.ee........eeeeee......eeeeeeeee..hhhhhhhhh......eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeee....eee....eeeeee.eee..eee.....ee.....eee...ee......eee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xkd C   10 GDKICIGYHANNSTTQVDTLLEKNVTVTHSVELLENQKEKRFCKIMNKAPLDLKDCTIEGWILGNPKCDLLLGDQSWSYIVERPNAQNGICYPGVLNELEELKAFIGSGERVERFEMFPKSTWAGVDTSRGVTNACPSYTIDSSFYRNLVWIVKTDSATYPVIKGTYNNTGTQPILYFWGVHHPLDTTVQDNLYGSGDKYVRMGTESMNFAKSPEIAARPAVNGQRSRIDYYWSVLRPGETLNVESNGNLIAPWYAYKFVSKGAVFKSDLPIENCDATCQTITGVLRTNKTFQNVSPLWIGECPKYVKSESLRLATGLRNVPQIAT  328
                                    19        29        39        49      | 58        68        78  |     87       96A       106       116      125A|     |133       143 |     152     | 161       171       181       191       201       211       221       231       241       251       261||     272       282       292       302       312       322      
                                                                        55A                       80A              96A                          125A|  130A           144A          157A                                                                                                      262|                                                                
                                                                                                                                                 125B                                                                                                                                          264                                                                


Chain D from PDB  Type:PROTEIN  Length:173
                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xkd D    1 GIFGAIAGFIEGGWTGMIDGWYGYHHENSQGSGYAADRESTQKAIDGITNKVNSIINKMNTQFEAVDHEFSNLERRIGNLNKRMEDGFLDVWTYNAELLVLLENERTLDLHDANVKNLYEKVKSQLRDNANDLGNGCFEFWHKCDNECMESVKNGTYDYPKYQKESKLNRQGI  173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain E from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhh.....ee...eee...........eee.hhhhhhhhhhh..eeeeee..hhhhh..ee.....................eee.ee........eeeeee......eeeeeeeee..hhhhhhhhh......eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeee.....eee....eeeeee.eee..eee.....ee.....eee...ee......eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xkd E    9 PGDKICIGYHANNSTTQVDTLLEKNVTVTHSVELLENQKEKRFCKIMNKAPLDLKDCTIEGWILGNPKCDLLLGDQSWSYIVERPNAQNGICYPGVLNELEELKAFIGSGERVERFEMFPKSTWAGVDTSRGVTNACPSYTIDSSFYRNLVWIVKTDSATYPVIKGTYNNTGTQPILYFWGVHHPLDTTVQDNLYGSGDKYVRMGTESMNFAKSPEIAARPAVNGQRSRIDYYWSVLRPGETLNVESNGNLIAPWYAYKFVSKKGAVFKSDLPIENCDATCQTITGVLRTNKTFQNVSPLWIGECPKYVKSESLRLATGLRNVPQ  325
                                    18        28        38        48       |57        67        77   |    86        96|      105       115       125||     132       142  |    151      |160       170       180       190       200       210       220       230       240       250       260  |    270       280       290       300       310       320     
                                                                         55A                       80A              96A                          125A|  130A           144A          157A                                                                                                      263B                                                              
                                                                                                                                                  125B                                                                                                                                                                                                           


Chain F from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xkd F    1 GIFGAIAGFIEGGWTGMIDGWYGYHHENSQGSGYAADRESTQKAIDGITNKVNSIINKMNTQFEAVDHEFSNLERRIGNLNKRMEDGFLDVWTYNAELLVLLENERTLDLHDANVKNLYEKVKSQLRDNANDLGNGCFEFWHKCDNECMESVKNGTYDYPKYQKESKLNRQG  172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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 4XKD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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 Related Entries

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

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        A0A0J9X267_9 | A0A0J9X267: 4xke 4xkf 4xkg 4yy0 4yy1 4yy7 4yy9 4yya 4yyb
        A0A0J9X268_9 | A0A0J9X268: 4xke 4xkf 4xkg 4yy0 4yy1 4yy7 4yy9 4yya 4yyb

(-) Related Entries Specified in the PDB File

4xke 4xkf 4xkg