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(-) Description

Title :  CRYSTAL STRUCTURE OF THE "AVIANIZED" 1918 INFLUENZA VIRUS HEMAGGLUTININ
 
Authors :  D. C. Ekiert, I. A. Wilson
Date :  04 Sep 12  (Deposition) - 19 Dec 12  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Viral Fusion Protein, Virus Attachment And Entry, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tsibane, D. C. Ekiert, J. C. Krause, O. Martinez, J. E. Crowe, I. A. Wilson, C. F. Basler
Influenza Human Monoclonal Antibody 1F1 Interacts With Thre Major Antigenic Sites And Residues Mediating Human Receptor Specificity In H1N1 Viruses.
Plos Pathog. V. 8 03067 2012
PubMed-ID: 23236279  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003067

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1 CHAIN
    Chains: A, C, E
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Strain: HIGH5
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 18-344
    Gene: HA
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 88776
    Strain: A/SOUTH CAROLINA/1/1918 H1N1
    Synonym: HEMAGGLUTININ RECEPTOR BINDING SUBUNIT
 
Molecule 2 - HEMAGGLUTININ HA2 CHAIN
    Chains: B, D, F
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Strain: HIGH5
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 345-520
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 88776
    Strain: A/SOUTH CAROLINA/1/1918 H1N1
    Synonym: HEMAGGLUTININ MEMBRANE FUSION SUBUNIT

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2MAN3Ligand/IonALPHA-D-MANNOSE
3NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:21BINDING SITE FOR RESIDUE NAG A 401
2AC2SOFTWAREASN C:21BINDING SITE FOR RESIDUE NAG C 401
3AC3SOFTWAREASN C:278 , ASN C:289BINDING SITE FOR RESIDUE NAG C 407
4AC4SOFTWAREASN E:21BINDING SITE FOR RESIDUE NAG E 401
5AC5SOFTWAREALA F:147 , GLU F:150 , ASN F:154 , THR F:156BINDING SITE FOR RESIDUE NAG F 201
6AC6SOFTWAREASN A:73 , GLU A:94 , ASN A:95 , CYS A:97 , LYS A:222 , VAL A:223 , ARG A:224 , HOH A:528 , HOH A:611 , HOH A:677 , HOH A:686 , HOH A:698BINDING SITE FOR LINKED RESIDUES A 402 to 405
7AC7SOFTWAREASN C:73 , GLU C:75 , GLU C:94 , ASN C:95 , CYS C:97 , LYS C:222 , ARG C:224 , HOH C:540 , HOH C:618 , HOH C:635 , HOH C:636 , HOH C:689BINDING SITE FOR LINKED RESIDUES C 402 to 406
8AC8SOFTWAREASN E:73 , GLU E:94 , ASN E:95 , CYS E:97 , ARG E:224 , HOH E:528 , HOH E:728BINDING SITE FOR LINKED RESIDUES E 402 to 404

(-) 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 4GXX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GXX)

(-) 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 d4gxxa_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......ee.......ee...eee.ee......eeee.....eeee..hhhhhhhhhhhhhhhh.......eee...............hhhhhhhhhh.eeeeeeee.................eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeeee.ee....ee.....ee.....eeeee.ee......eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gxx A   10 GDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTEQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRGQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIP  324
                                    19        29        39        49     |  58        68        78     |  87        96       106       116      125A||     133|      142       152       162       172       182       192       202       212       222       232       242       252       262  |    271       281       291       301       311       321   
                                                                       54A                           83A          95A                           125A||     133A                                                                                                                                264A                                                            
                                                                                                                                                 125B|                                                                                                                                                                                                         
                                                                                                                                                  125C                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                           
               SCOP domains d4gxxb_ B: Influenza hemagglutinin (stalk)                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gxx B    1 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNR  170
                                    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 d4gxxc_ C: Hemagglutinin                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......ee.......ee...eee.ee......eee......eeee..hhhhhhhhhhhhhhhhhh.....eee...............hhhhhhhhhh.eeeeeeee..hhhhhh.........eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeee..eee..eee.....ee.....eeeee.ee......eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gxx C   11 DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTEQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRGQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPS  325
                                    20        30        40        50    |   59        69        79    |   88       |97       107       117      125B|     133A       143       153       163       173       183       193       203       213       223       233       243       253       263 |     272       282       292       302       312       322   
                                                                      54A                           83A          95A                           125A||     133A                                                                                                                                264A                                                             
                                                                                                                                                125B|                                                                                                                                                                                                          
                                                                                                                                                 125C                                                                                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                           
               SCOP domains d4gxxd_ D: Influenza hemagglutinin (stalk)                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gxx D    1 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNR  170
                                    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 d4gxxe_ E: Hemagglutinin                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...............hhhhhhhhhh.eeeeeeee.................eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeeee.eee..eee.....ee......ee...ee......eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gxx E    9 PGDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTEQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRGQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPS  325
                                    18        28        38        48      | 57        67        77      | 86       95A       105       115       125|||    132 |     141       151       161       171       181       191       201       211       221       231       241       251       261   |   270       280       290       300       310       320     
                                                                        54A                           83A          95A                           125A||     133A                                                                                                                                264A                                                             
                                                                                                                                                  125B|                                                                                                                                                                                                          
                                                                                                                                                   125C                                                                                                                                                                                                          


Chain F from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                            
               SCOP domains d4gxxf_ F: Influenza hemagglutinin (stalk)                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gxx F    1 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNRE  171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   Legend:   → Mismatch (orange background)
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  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  (2, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  4gxx
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  HEMA_I18A0 | Q9WFX3
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 Related Entries

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

UniProtKB/Swiss-Prot
        HEMA_I18A0 | Q9WFX3: 1rd8 1ruz 2wrg 3gbn 3lzf 3r2x 4eef 4gxu 4jug 4juh 4juj 4py8

(-) Related Entries Specified in the PDB File

4gxu 4gxv