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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DESIGNED INHIBITOR PROTEIN F-HB80.4 IN COMPLEX WITH THE 1918 INFLUENZA VIRUS HEMAGGLUTININ.
 
Authors :  C. Dreyfus, I. A. Wilson
Date :  28 Mar 12  (Deposition) - 27 Jun 12  (Release) - 27 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I
Biol. Unit 1:  A,B,G  (1x)
Biol. Unit 2:  C,D,H  (1x)
Biol. Unit 3:  E,F,I  (1x)
Biol. Unit 4:  A,B,C,D,E,F,G,H,I  (1x)
Keywords :  Immunoglobulin, Hemagglutinin, Fusion Of Virus Membrane With Host Membrane, Membrane Fusion, Sialic Acid, Virion, Immune System, Immune System-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Whitehead, A. Chevalier, Y. Song, C. Dreyfus, S. J. Fleishman, C. De Mattos, C. A. Myers, H. Kamisetty, P. Blair, I. A. Wilson, D. Bake
Optimization Of Affinity, Specificity And Function Of Designed Influenza Inhibitors Using Deep Sequencing.
Nat. Biotechnol. V. 30 543 2012
PubMed-ID: 22634563  |  Reference-DOI: 10.1038/NBT.2214

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1 CHAIN
    Chains: A, C, E
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Strain: HIGH FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: HA, HEMAGGLUTININ
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 88776
    Strain: A/SOUTH CAROLINA/1/1918 (H1N1)
    Synonym: HEMAGGLUTININ HA1 CHAIN
 
Molecule 2 - HEMAGGLUTININ HA2 CHAIN
    Chains: B, D, F
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Strain: HIGH FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: HA, HEMAGGLUTININ
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 88776
    Strain: A/SOUTH CAROLINA/1/1918 (H1N1)
    Synonym: HEMAGGLUTININ HA2 CHAIN
 
Molecule 3 - F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN
    Chains: G, H, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA 2 (BL21/DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTIFICIAL GENE
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFGHI
Biological Unit 1 (1x): AB    G  
Biological Unit 2 (1x):   CD   H 
Biological Unit 3 (1x):     EF  I
Biological Unit 4 (1x): ABCDEFGHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (2, 9)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:73 , GLU A:75 , GLU A:94 , ASN A:95 , CYS A:97 , ARG A:224 , NAG A:402BINDING SITE FOR RESIDUE NAG A 401
2AC2SOFTWAREARG A:224 , NAG A:401 , BMA A:403BINDING SITE FOR RESIDUE NAG A 402
3AC3SOFTWARENAG A:402BINDING SITE FOR RESIDUE BMA A 403
4AC4SOFTWAREASN C:73 , GLU C:75 , GLU C:94 , ASN C:95 , CYS C:97 , ARG C:224 , NAG C:402BINDING SITE FOR RESIDUE NAG C 401
5AC5SOFTWARENAG C:401 , BMA C:403BINDING SITE FOR RESIDUE NAG C 402
6AC6SOFTWARENAG C:402BINDING SITE FOR RESIDUE BMA C 403
7AC7SOFTWAREASN E:73 , GLU E:94 , ASN E:95 , CYS E:97 , ARG E:224 , NAG E:402BINDING SITE FOR RESIDUE NAG E 401
8AC8SOFTWAREARG E:224 , NAG E:401 , BMA E:403BINDING SITE FOR RESIDUE NAG E 402
9AC9SOFTWARENAG E:402BINDING SITE FOR RESIDUE BMA E 403

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:52 -A:277
2A:64 -A:76
3A:97 -A:139
4A:281 -A:305
5B:144 -B:148
6C:52 -C:277
7C:64 -C:76
8C:97 -C:139
9C:281 -C:305
10D:144 -D:148
11E:14 -F:137
12E:52 -E:277
13E:64 -E:76
14E:97 -E:139
15E:281 -E:305
16F:144 -F:148

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EEF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EEF)

(-) 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:325
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..ee.......ee.......ee...eee.ee......eee......ee....hhhhhhhhhhhhhhhhhh.....eee...............hhhhhhhhhh.eeeeeeee..hhhhhh.........eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeee..ee....ee.....ee......ee...ee......eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4eef A   10 GDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPSI  326
                                    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:173
                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee.....eeee..hhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeee....hhhhhhhhhhh..hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4eef B    1 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEI  173
                                    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 ..eeeeeee......ee.......ee...eee.ee......eeee.....eeee..hhhhhhhhhhhhhhhhhh.....eee...............hhhhhhhhhh.eeeeeeee.................eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeeee.ee...........ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4eef C   10 GDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIP  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 D from PDB  Type:PROTEIN  Length:173
                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee.......eee..ee..ee..ee..hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4eef D    1 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEI  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:323
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eee......ee....hhhhhhhhhhhhhhhhhh.....eee...............hhhhhhhhhh.eeeeeeee..........ee.....eeeeee..eee....eee.ee.......eeeeee......eeeeeeeee..hhhhhhhhh......eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeee..ee...........ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4eef E   10 GDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIP  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 F from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeee........eeehhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eee..eee..................hhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4eef F    1 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNRE  171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 


Chain G from PDB  Type:PROTEIN  Length:45
                                                                              
               SCOP domains --------------------------------------------- SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.............hhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                4eef G   10 PWKFSENIAFEIALSFTNKDTPDRWKKVAQYVKGRTPEEVKKHYE   54
                                    19        29        39        49     


Chain H from PDB  Type:PROTEIN  Length:47
                                                                                
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh........hhhhhhhh.....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                4eef H    8 GRPWKFSENIAFEIALSFTNKDTPDRWKKVAQYVKGRTPEEVKKHYE   54
                                    17        27        37        47       


Chain I from PDB  Type:PROTEIN  Length:47
                                                                                
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.....hhhhhhhh.....hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                4eef I    8 GRPWKFSENIAFEIALSFTNKDTPDRWKKVAQYVKGRTPEEVKKHYE   54
                                    17        27        37        47
   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 4EEF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

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  4eef
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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 4gxu 4gxx 4jug 4juh 4juj 4py8

(-) Related Entries Specified in the PDB File

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