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(-) Description

Title :  CRYSTAL STRUCTURE OF H5 HEMAGGLUTININ Q226L MUTANT FROM THE INFLUENZA VIRUS A/DUCK/EGYPT/10185SS/2010 (H5N1) WITH LSTA
 
Authors :  X. Zhu, I. A. Wilson
Date :  01 Oct 15  (Deposition) - 02 Dec 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  H5N1 Influenza Virus, Hemagglutinin, Receptor Binding Specificity, Transmission, Glycan Complex, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhu, K. Viswanathan, R. Raman, W. Yu, R. Sasisekharan, I. A. Wilson
Structural Basis For A Switch In Receptor Binding Specificity Of Two H5N1 Hemagglutinin Mutants.
Cell Rep V. 13 1683 2015
PubMed-ID: 26586437  |  Reference-DOI: 10.1016/J.CELREP.2015.10.027

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: C, A, E
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PFASTBAC-HT
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 17-345
    Gene: HA
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS (A/DUCK/EGYPT/10185SS/2010(H5N1))
    Organism Taxid: 1092915
    Strain: A/DUCK/EGYPT/10185SS/2010(H5N1)
    Synonym: HEMAGGLUTININ HA1 CHAIN
 
Molecule 2 - HEMAGGLUTININ
    Chains: D, B, F
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: BACULOVIRUS
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 347-520
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 1092915
    Strain: A/DUCK/EGYPT/10185SS/2010(H5N1)
    Synonym: HEMAGGLUTININ HA2 CHAIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric/Biological Unit (5, 20)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2FUL3Ligand/IonBETA-L-FUCOSE
3GAL3Ligand/IonBETA-D-GALACTOSE
4NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:33binding site for Mono-Saccharide NAG A 1001 bound to ASN A 33
2AC2SOFTWAREASN A:169 , ASN A:240 , HOH A:1145 , GLY C:49 , SER E:221binding site for Poly-Saccharide residues NAG A 1002 through NAG A 1005 bound to ASN A 169
3AC3SOFTWAREGLN C:25 , ASN C:33binding site for Mono-Saccharide NAG C 1001 bound to ASN C 33
4AC4SOFTWAREASN C:169 , ASN C:240binding site for Poly-Saccharide residues NAG C 1002 through NAG C 1004 bound to ASN C 169
5AC5SOFTWAREGLN E:25 , ASN E:33binding site for Mono-Saccharide NAG E 1001 bound to ASN E 33
6AC6SOFTWAREASN E:169 , ASN E:240 , ASP E:241 , HOH E:1113binding site for Poly-Saccharide residues NAG E 1002 through NAG E 1004 bound to ASN E 169
7AC7SOFTWARETYR A:98 , GLY A:134 , VAL A:135 , SER A:136 , SER A:137 , TRP A:153 , HIS A:183 , GLU A:190 , ARG A:193 , LEU A:194 , LYS A:222 , LEU A:226 , HOH A:1110 , HOH A:1114 , HOH A:1133binding site for Poly-Saccharide residues SIA A 1006 through NAG A 1008
8AC8SOFTWARETYR A:98 , GLY A:134 , VAL A:135 , SER A:136 , SER A:137 , TRP A:153 , HIS A:183 , GLU A:190 , ARG A:193 , LEU A:194 , LYS A:222 , LEU A:226 , NAG A:1002 , FUC A:1003 , FUL A:1004 , HOH A:1110 , HOH A:1114 , HOH A:1133 , TYR C:98 , VAL C:135 , SER C:136 , SER C:137 , HIS C:183 , GLU C:190 , ARG C:193 , LEU C:194 , GLY C:225binding site for Poly-Saccharide residues SIA C 1005 through GAL C 1006
9AC9SOFTWARETYR E:98 , VAL E:135 , SER E:136 , SER E:137 , HIS E:183 , GLU E:190 , ARG E:193binding site for Poly-Saccharide residues SIA E 1005 through GAL E 1006

(-) SS Bonds  (18, 18)

Asymmetric/Biological 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:64 -E:76
16E:97 -E:139
17E:281 -E:305
18F:144 -F:148

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E2Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E2Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E2Z)

(-) Exons   (0, 0)

(no "Exon" information available for 5E2Z)

(-) 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:323
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhh..eeeeeeee..hhhhh........eeeee....ee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeeee....eee....eeeeee.eee..ee......ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5e2z A    8 DPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCNLDGVKPLILRDCSVAGWLLGNPMCDEFLNVPEWSYIVEKINPANDLCYPGNFNDYEELKHLLSRINHFEKIQITPKNSWSDHEASGVSSACPYQGRSSFFRNVVWLTKKDNAYPTIKRSYNNTNQEDLLVLWGIHHPNDATEQTRLYQNPTTYISVGTSTLNQKLVPKIATRSKVKGLSGRMEFFWTILKSNDAINFESNGNFIAPENAYKIVKKGDSTIMKSELEYGDCNTKCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP  324
                                    17        27        37        47        56        66        76       |85        95 |     104       114       124 ||    132       142       152       162       172       182       192       202       212       222       232       242       252       261       271       281       291       301       311       321   
                                                                          55A                          83A           96A                          125A|                                                                                                                                    260A                                                                
                                                                                                                                                   125B                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee......eeehhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee.......hhhhhhh.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5e2z B    1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHRCDNECMESVRNGTYDYPQYSEEARLKREEISG  175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain C from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhhh.eeeeeeee..hhhhh...ee...eeeee....ee....eeeee........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeeee....eee....eeeeee.eee..ee......ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5e2z C    8 DPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCNLDGVKPLILRDCSVAGWLLGNPMCDEFLNVPEWSYIVEKINPANDLCYPGNFNDYEELKHLLSRINHFEKIQITPKNSWSDHEASGVSSACPYQGRSSFFRNVVWLTKKDNAYPTIKRSYNNTNQEDLLVLWGIHHPNDATEQTRLYQNPTTYISVGTSTLNQKLVPKIATRSKVKGLSGRMEFFWTILKSNDAINFESNGNFIAPENAYKIVKKGDSTIMKSELEYGDCNTKCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP  324
                                    17        27        37        47        56        66        76       |85        95 |     104       114       124 ||    132       142       152       162       172       182       192       202       212       222       232       242       252       261       271       281       291       301       311       321   
                                                                          55A                          83A           96A                          125A|                                                                                                                                    260A                                                                
                                                                                                                                                   125B                                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee......eeehhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee.......hhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5e2z D    1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHRCDNECMESVRNGTYDYPQYSEEARLKREEISG  175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain E from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhh..eeeeeeee..hhhhh..ee....eeeee....ee....eee.ee.......eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeeee....eee....eeeeee.eee..ee......ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5e2z E    8 DPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCNLDGVKPLILRDCSVAGWLLGNPMCDEFLNVPEWSYIVEKINPANDLCYPGNFNDYEELKHLLSRINHFEKIQITPKNSWSDHEASGVSSACPYQGRSSFFRNVVWLTKKDNAYPTIKRSYNNTNQEDLLVLWGIHHPNDATEQTRLYQNPTTYISVGTSTLNQKLVPKIATRSKVKGLSGRMEFFWTILKSNDAINFESNGNFIAPENAYKIVKKGDSTIMKSELEYGDCNTKCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP  324
                                    17        27        37        47        56        66        76       |85        95 |     104       114       124 ||    132       142       152       162       172       182       192       202       212       222       232       242       252       261       271       281       291       301       311       321   
                                                                          55A                          83A           96A                          125A|                                                                                                                                    260A                                                                
                                                                                                                                                   125B                                                                                                                                                                                                        


Chain F from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee......eeehhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee.......hhhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5e2z F    1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHRCDNECMESVRNGTYDYPQYSEEARLKREEISG  175
                                    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 5E2Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E2Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E2Z)

(-) 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
        G8IPF0_9INFA | G8IPF0: 5e2y 5e30

(-) Related Entries Specified in the PDB File

5e2y
5e30
5e32
5e34
5e35
5w2y THIS ENTRY CONTAINS THE SAME PROTEIN WITH 5E2Y, BUT COMPLEXED WITH LSTA.