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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB CR6261 IN COMPLEX WITH THE 1918 H1N1 INFLUENZA VIRUS HEMAGGLUTININ
 
Authors :  D. C. Ekiert, M. A. Elsliger, I. A. Wilson
Date :  20 Feb 09  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  A,B,H,L  (3x)
Keywords :  Hemagglutinin, Fab, Neutralizing Antibodies, Antibody, Pandemic Flu, Cell Membrane, Envelope Protein, Fusion Protein, Glycoprotein, Lipoprotein, Membrane, Palmitate, Transmembrane, Virion, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. C. Ekiert, G. Bhabha, M. A. Elsliger, R. H. Friesen, M. Jongeneelen, M. Throsby, J. Goudsmit, I. A. Wilson
Antibody Recognition Of A Highly Conserved Influenza Virus Epitope.
Science V. 324 246 2009
PubMed-ID: 19251591  |  Reference-DOI: 10.1126/SCIENCE.1171491

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: A
    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: RECEPTOR BINDING DOMAIN, HA1
    Gene: HA, HEMAGGLUTININ (HA)
    Organism Common: INFLUENZA A VIRUS (STRAIN A/SOUTH CAROLINA/1/1918 H1N1)
    Organism Scientific: INFLUENZA A VIRUS (A/BREVIG MISSION/1/1918(H1N1))
    Organism Taxid: 88776
    Strain: A/SOUTH CAROLINA/1/1918
    Synonym: HEMAGGLUTININ HA1 CHAIN, HEMAGGLUTININ HA2 CHAIN
 
Molecule 2 - HEMAGGLUTININ
    Chains: B
    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: MEMBRANE FUSION DOMAIN, HA2
    Gene: HA, HEMAGGLUTININ (HA)
    Organism Common: INFLUENZA A VIRUS (STRAIN A/SOUTH CAROLINA/1/1918 H1N1)
    Organism Scientific: INFLUENZA A VIRUS (A/BREVIG MISSION/1/1918(H1N1))
    Organism Taxid: 88776
    Strain: A/SOUTH CAROLINA/1/1918
    Synonym: HEMAGGLUTININ HA1 CHAIN, HEMAGGLUTININ HA2 CHAIN
 
Molecule 3 - FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - FAB LAMBDA LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (3x): ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 16)

Asymmetric Unit (8, 16)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL1Ligand/IonCHLORIDE ION
3EDO5Ligand/Ion1,2-ETHANEDIOL
4ETX1Ligand/Ion2-ETHOXYETHANOL
5GOL2Ligand/IonGLYCEROL
6MAN1Ligand/IonALPHA-D-MANNOSE
7NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
8UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (7, 45)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2CL-1Ligand/IonCHLORIDE ION
3EDO15Ligand/Ion1,2-ETHANEDIOL
4ETX3Ligand/Ion2-ETHOXYETHANOL
5GOL6Ligand/IonGLYCEROL
6MAN3Ligand/IonALPHA-D-MANNOSE
7NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
8UNL3Ligand/IonUNKNOWN LIGAND

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARENAG A:2 , BMA A:3 , MAN A:4 , ASN A:21BINDING SITE FOR RESIDUE NAG A 1
02AC2SOFTWARENAG A:1 , BMA A:3 , ASN A:21BINDING SITE FOR RESIDUE NAG A 2
03AC3SOFTWARENAG A:1 , NAG A:2 , MAN A:4 , ILE B:18BINDING SITE FOR RESIDUE BMA A 3
04AC4SOFTWARENAG A:1 , BMA A:3 , HIS A:18 , ASN A:20 , ASN A:21 , HIS A:38 , PHE H:54BINDING SITE FOR RESIDUE MAN A 4
05AC5SOFTWAREASN A:73 , GLU A:75 , ASN A:95 , CYS A:97 , ARG A:224 , HOH A:379BINDING SITE FOR RESIDUE NAG A 330
06AC6SOFTWAREVAL A:26 , ASP A:27 , LYS A:313 , ARG A:315 , ASN B:104BINDING SITE FOR RESIDUE EDO A 331
07AC7SOFTWAREARG A:321 , HOH A:361 , HOH A:398 , GLY B:1 , ILE B:6BINDING SITE FOR RESIDUE GOL A 332
08AC8SOFTWAREVAL A:29 , LEU A:30 , LYS B:51 , LEU B:102 , GLU B:103 , GLU B:105 , ARG B:106 , HOH B:226 , HOH B:270BINDING SITE FOR RESIDUE ETX A 333
09AC9SOFTWAREALA B:147 , GLU B:150 , ASN B:154 , HOH B:274BINDING SITE FOR RESIDUE NAG B 180
10BC1SOFTWAREALA B:36 , ASP B:37 , GLN B:38 , LYS B:39 , GLU B:150 , ARG B:153 , EDO B:183 , HOH B:300BINDING SITE FOR RESIDUE GOL B 181
11BC2SOFTWARETYR B:24 , HIS B:26 , GLY B:33 , ARG B:153 , HOH B:273BINDING SITE FOR RESIDUE CL B 182
12BC3SOFTWARETYR B:24 , ASP B:37 , ARG B:153 , ASN B:154 , GLY B:155 , GOL B:181 , HOH B:207 , HOH B:289BINDING SITE FOR RESIDUE EDO B 183
13BC4SOFTWAREGLY B:1 , ASN B:114 , ASN B:117BINDING SITE FOR RESIDUE EDO B 184
14BC5SOFTWAREASP A:11 , ASN B:28 , GLU B:29 , GLN B:30 , LYS B:143 , ASP B:145BINDING SITE FOR RESIDUE EDO B 185
15BC6SOFTWAREARG B:116 , TYR B:119 , GLU B:120 , LYS B:123 , SER B:124 , GLU B:132 , HOH B:278 , HOH B:291BINDING SITE FOR RESIDUE UNL B 186
16BC7SOFTWAREHOH B:284 , GLY H:27 , PHE H:29 , ARG H:30 , SER H:31 , HOH H:294 , HOH H:302BINDING SITE FOR RESIDUE EDO H 228

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:14 -B:137
2A:52 -A:277
3A:64 -A:76
4A:97 -A:139
5A:281 -A:305
6B:144 -B:148
7H:22 -H:92
8L:23 -L:88
9L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ala A:7 -Asp A:8
2Lys A:133A-Gly A:134
3Gly A:134 -Val A:135
4Gly A:188 -Thr A:189
5Gly H:27 -Pro H:28
6Pro H:41 -Gly H:42
7Lys H:145 -Asp H:146
8Phe H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GBN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GBN)

(-) Exons   (0, 0)

(no "Exon" information available for 3GBN)

(-) 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:328
 aligned with HEMA_I18A0 | Q9WFX3 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:328
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333        
          HEMA_I18A0     14 ATNADTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPSI  341
               SCOP domains d3gbna_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3gbnA01 A:7-51,A:276-326                     3gbnA02 A:52-275  [code=3.90.209.20, no name defined]                                                                                                                                                                                   3gbnA01 A:7-51,A:276-326                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.......ee.......ee...eee.ee......eee......eeee..hhhhhhhhhhhhhhhh.......eee...............hhhhhhhhhh.eeeeeeee.................eeeee....ee....eee..........eeeeee......eeeeeeeee....hhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeee..eee..eee.....ee......ee...ee......eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gbn A    7 ADPGDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPSI  326
                                    16        26        36        46        55        65        75        84        94 |     103       113       123  |||  130   |   139       149       159       169       179       189       199       209       219       229       239       249       259     | 268       278       288       298       308       318        
                                                                          54A                           83A          95A                           125A||     133A                                                                                                                                264A                                                              
                                                                                                                                                    125B|                                                                                                                                                                                                           
                                                                                                                                                     125C                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with HEMA_I18A0 | Q9WFX3 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:173
                                   354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514   
          HEMA_I18A0    345 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEI  517
               SCOP domains d3gbnb_ B: Influenza hemagglutinin (stalk)                                                                                                                                    SCOP domains
               CATH domains 3gbnB00 B:1-173  [code=3.90.20.10, no name defined]                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gbn B    1 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEI  173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain H from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3gbnH01 H:1-113 Immunoglobulins                                                                                          --------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee.....eeeeeee.........eeeeee......eeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee........eeee...eeeee........eee....eeeee..........ee.....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gbn H    1 EVQLVESGAEVKKPGSSVKVSCKASGGPFRSYAISWVRQAPGQGPEWMGGIIPIFGTTKYAPKFQGRVTITADDFAGTVYMELSSLRSEDTAMYYCAKHMGYQVRETMDVWGKGTTVTVSSASTKGPSVFPLGCLVKDYFPEPVTTFPAVLQSSGLYSLS  188
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122 ||    148    || 177  ||   188
                                                                              52A                            82A||               100A|||                     124|         153|    180|      
                                                                                                              82B|                100B||                      141          173     182      
                                                                                                               82C                 100C|                                                    
                                                                                                                                    100D                                                    


Chain L from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                        
               SCOP domains d3gbnl1 L:3-106A automated matches                                                                           ------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.....eeeeee....hhhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee.....eeee...eeeee..........eeeeeeee..eeeeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gbn L    3 VLTQPPSVSAAPGQKVTISCSGSSSNIGNDYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEANYYCATWDRRPTAYVVFGGGTKLTVLEELQANKATLVCLISDFYGVETTTPSKQSNNKYAASSYLSCQ  195
                                  ||13        23    ||  31        41        51        61        71        81        91    ||| 98       123       133      |160       171       194 
                                  9|              27A|                                                                  95A||        106A|              140|       168|       180| 
                                  11               27B                                                                   95B|          123               158        170        194 
                                                                                                                          95C
   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  (3, 3)

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

(-) CATH Domains  (4, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GBN)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HEMA_I18A0 | Q9WFX3)
molecular function
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0019065    receptor-mediated endocytosis of virus by host cell    Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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  Cis Peptide Bonds
    Ala A:7 - Asp A:8   [ RasMol ]  
    Gly A:134 - Val A:135   [ RasMol ]  
    Gly A:188 - Thr A:189   [ RasMol ]  
    Gly H:27 - Pro H:28   [ RasMol ]  
    Lys A:133A - Gly A:134   [ RasMol ]  
    Lys H:145 - Asp H:146   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
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  HEMA_I18A0 | Q9WFX3
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        HEMA_I18A0 | Q9WFX3: 1rd8 1ruz 2wrg 3lzf 3r2x 4eef 4gxu 4gxx 4jug 4juh 4juj 4py8

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3gbm