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(-) Description

Title :  CRYSTAL STRUCTURE OF A 2009 H1N1 INFLUENZA VIRUS HEMAGGLUTININ WITH A STABILIZATION MUTATION HA2 E47G
 
Authors :  X. Zhu, I. A. Wilson
Date :  07 Aug 13  (Deposition) - 25 Sep 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Viral Envelope Protein, Viral Fusion Protein, Stabilization Mutant, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hong, P. S. Lee, R. M. Hoffman, X. Zhu, J. C. Krause, N. S. Laursen, S. I. Yoon, L. Song, L. Tussey, J. E. Crowe, A. B. Ward, I. A. Wilson
Antibody Recognition Of The Pandemic H1N1 Influenza Virus Hemagglutinin Receptor Binding Site.
J. Virol. V. 87 12471 2013
PubMed-ID: 24027321  |  Reference-DOI: 10.1128/JVI.01388-13

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1 SUBUNIT
    Chains: A, C, 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: ECTODOMAIN (RESIDUES 18-344)
    Gene: HA, HEMAGGLUTININ
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 641501
    Strain: A/CALIFORNIA/04/2009
 
Molecule 2 - HEMAGGLUTININ HA2 SUBUNIT
    Chains: B, D, F
    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: ECTODOMAIN (RESIDUES 345-518)
    Gene: HA, HEMAGGLUTININ
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 641501
    Strain: A/CALIFORNIA/04/2009

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2FUL1Ligand/IonBETA-L-FUCOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:73 , ASP A:93 , ASN A:94 , CYS A:97 , PRO A:140 , ARG A:224 , HOH A:521BINDING SITE FOR RESIDUE NAG A 401
02AC2SOFTWAREASP A:276 , ASN A:278 , HOH A:648BINDING SITE FOR RESIDUE NAG A 402
03AC3SOFTWAREASN A:21 , GLU A:261 , HOH A:641BINDING SITE FOR RESIDUE NAG A 403
04AC4SOFTWAREASN C:73 , GLU C:75 , ASP C:93 , ASN C:94 , CYS C:97 , ARG C:224BINDING SITE FOR RESIDUE NAG C 401
05AC5SOFTWAREASP C:276 , ASN C:278BINDING SITE FOR RESIDUE NAG C 402
06AC6SOFTWAREASN C:33 , NAG C:404 , HOH C:674BINDING SITE FOR RESIDUE NAG C 403
07AC7SOFTWARELYS A:50 , PRO A:273 , NAG C:403 , BMA C:405BINDING SITE FOR RESIDUE NAG C 404
08AC8SOFTWAREGLY A:49 , LYS A:50 , PRO A:273 , NAG C:404 , MAN C:406 , HOH C:625 , HOH C:627BINDING SITE FOR RESIDUE BMA C 405
09AC9SOFTWAREGLY A:49 , THR A:272 , LYS A:285 , BMA C:405BINDING SITE FOR RESIDUE MAN C 406
10BC1SOFTWAREASN C:21BINDING SITE FOR RESIDUE NAG C 407
11BC2SOFTWAREASN E:73 , GLU E:75 , ASP E:93 , ASN E:94 , CYS E:97 , ARG E:224 , HOH E:626BINDING SITE FOR RESIDUE NAG E 401
12BC3SOFTWAREASP E:276 , ASN E:278BINDING SITE FOR RESIDUE NAG E 402
13BC4SOFTWAREASP B:158 , LYS B:161 , ASN E:21 , NAG E:404 , FUL E:405BINDING SITE FOR RESIDUE NAG E 403
14BC5SOFTWAREASP B:158 , NAG E:403 , FUL E:405BINDING SITE FOR RESIDUE NAG E 404
15BC6SOFTWAREASP B:158 , PRO B:160 , NAG E:403 , NAG E:404BINDING SITE FOR RESIDUE FUL E 405

(-) 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 4M4Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M4Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M4Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4M4Y)

(-) 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:324
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4m4ya_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhh..........eee...............hhhhhhhhhh.eeeeeeee..hhhhhh.........eeeeee..eee....eee..........eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeeee.eee..ee......ee......ee...ee......eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4m4y A   10 GDTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPS  325
                                    19        29        39        49      | 58        68        78     |  87   |    96       106       116|||    123       133|      142       152       162       172       182       192       202       212       222       232       242       252       262    |  271       281       291       301       311       321    
                                                                        55A                          83A     90A                       116A||              133A                                                                                                                                  266A                                                           
                                                                                                                                        116B|                                                                                                                                                                                                                   
                                                                                                                                         116C                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                                
               SCOP domains d4m4yb_ B: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m4y B    1 GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDS  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 d4m4yc_ C: Hemagglutinin                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhh..........eee...............hhhhhhhhhh.eeeeeeee..hhhhhh.........eeeeee..eee....eee..........eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeeee.eee..ee......ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m4y C   10 GDTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIP  324
                                    19        29        39        49      | 58        68        78     |  87   |    96       106       116|||    123       133|      142       152       162       172       182       192       202       212       222       232       242       252       262    |  271       281       291       301       311       321   
                                                                        55A                          83A     90A                       116A||              133A                                                                                                                                  266A                                                          
                                                                                                                                        116B|                                                                                                                                                                                                                  
                                                                                                                                         116C                                                                                                                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                            
               SCOP domains d4m4yd_ D: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m4y D    1 GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNRE  171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 


Chain E from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4m4ye_ E: Hemagglutinin                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhh..........eee...............hhhhhhhhhh.eeeeeeee.................eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeeee.eee..ee......ee......ee...ee......eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m4y E    8 DPGDTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPS  325
                                    17        27        37        47        56        66        76       |85     |  94       104       114  |||  121       131  |    140       150       160       170       180       190       200       210       220       230       240       250       260      |269       279       289       299       309       319      
                                                                          55A                          83A     90A                       116A||              133A                                                                                                                                  266A                                                           
                                                                                                                                          116B|                                                                                                                                                                                                                   
                                                                                                                                           116C                                                                                                                                                                                                                   


Chain F from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                            
               SCOP domains d4m4yf_ F: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeee....hhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m4y F    1 GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNRE  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 4M4Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M4Y)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  4m4y
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 Related Entries

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

UniProtKB/TrEMBL
        C3W5S1_I09A0 | C3W5S1: 3al4 3lzg 3ube 3ubj 3ubn 3ubq 3uyw 3uyx 3ztn 4jtv 4jtx 4ju0 5gjs 5k9o

(-) Related Entries Specified in the PDB File

3lzg 2009 H1N1 INFLUENZA VIRUS HEMAGGLUTININ WITH A SINGLE MUTATION