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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB 8F8 IN COMPLEX A H2N2 INFLUENZA VIRUS HEMAGGLUTININ
 
Authors :  R. Xu, I. A. Wilson
Date :  04 Oct 12  (Deposition) - 13 Feb 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  A,B,H,L  (3x)
Keywords :  Viral Protein/Immune System, Hemagglutinin, Antibody, Viral Receptor Binding, Antigen Binding, Sialic Acid, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Xu, J. C. Krause, R. Mcbride, J. C. Paulson, J. E. Crowe, I. A. Wilson
A Recurring Motif For Antibody Recognition Of The Receptor-Binding Site Of Influenza Hemagglutinin.
Nat. Struct. Mol. Biol. V. 20 363 2013
PubMed-ID: 23396351  |  Reference-DOI: 10.1038/NSMB.2500

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI5
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7111
    Expression System Vector Type: AUTOGRAPHA CALIFORNICA NUCLEOPOLYHEDROVIRUS
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 382813
    Strain: A/JAPAN/305+/1957(H2N2)
 
Molecule 2 - HEMAGGLUTININ HA2
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI5
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7111
    Expression System Vector Type: AUTOGRAPHA CALIFORNICA NUCLEOPOLYHEDROVIRUS
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 382813
    Strain: A/JAPAN/305+/1957(H2N2)
 
Molecule 3 - FAB 8F8 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Common: HUMAN
    Expression System Plasmid: PEE6.4
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - FAB 8F8 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Common: HUMAN
    Expression System Plasmid: PEE12.4
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2MAN3Ligand/IonALPHA-D-MANNOSE
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:169 , THR A:242 , NAG A:402BINDING SITE FOR RESIDUE NAG A 401
2AC2SOFTWARETRP A:240 , NAG A:401 , BMA A:403 , MAN A:404BINDING SITE FOR RESIDUE NAG A 402
3AC3SOFTWARENAG A:402 , MAN A:404BINDING SITE FOR RESIDUE BMA A 403
4AC4SOFTWARENAG A:402 , BMA A:403BINDING SITE FOR RESIDUE MAN A 404
5AC5SOFTWAREGLU A:278 , ASN A:289 , NAG A:406BINDING SITE FOR RESIDUE NAG A 405
6AC6SOFTWARENAG A:405BINDING SITE FOR RESIDUE NAG A 406

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:14 -B:137
2A:52 -A:277
3A:64 -A:76
4A:281 -A:305
5B:144 -B:148
6H:22 -H:92
7L:23 -L:88
8L:134 -L:193

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Phe H:146 -Pro H:147
2Leu L:95 -Ser L:95A
3Tyr L:140 -Pro L:141
4Lys L:186 -Ser L:187
5Ser L:187 -His L:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HF5)

(-) Exons   (0, 0)

(no "Exon" information available for 4HF5)

(-) 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:324
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4hf5a_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee.ee.......ee.......ee...eee.........eeee.....ee....hhhhhhh.....hhhhh......eee...........eee.hhhhhhhhhhh...eeeee..hhhhh..ee...eeeeeee..eee....eee.ee.......eeeeee......eeeeeeeee..hhhhhhhhhh.....eeeee..eeeee...............eeeeeeeee....eeeeee...eeee.eeeee.......eee....eeeeee.eee..eee.....ee......ee...ee......eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4hf5 A    9 PGDQICIGYHANNSTEKVDTILERNVTVTHAKDILEKTHNGKLCKLNGIPPLELGDCSIAGWLLGNPECDRLLSVPEWSYIMEKENPRDGLCYPGSFNDYEELKHLLSSVKHFEKVKILPKDRWTQHTTTGGSRACAVSGNPSFFRNMVWLTEKGSNYPVAKGSYNNTSGEQMLIIWGVHHPNDETEQRTLYQNVGTYVSVGTSTLNKRSTPEIATRPKVNGQGGRMEFSWTLLDMWDTINFESTGNLIAPEYGFKISKRGSSGIMKTEGTLENCETKCQTPLGAINTTLPFHNVHPLTIGECPKYVKSEKLVLATGLRNVPQI  326
                                    18        28        38        48     |  57        67        77    |   86       95A       105       115 |||   122||     133       143       153       163       173       183       193       203       213       223       233       243       253       263|      272       282       292       302       312       322    
                                                                       53A                          81A            95A                  116A||    123|                                                                                                                                       263A                                                               
                                                                                                                                         116B|     125                                                                                                                                                                                                          
                                                                                                                                          116C                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                             
               SCOP domains d4hf5b_ B: Influenza hemagglutinin (stalk)                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee......hhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hf5 B    1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNDQGSGYAADKESTQKAFDGITNKVNSVIEKMNTQFEAVGKEFSNLERRLENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRMQLRDNVKELGNGCFEFYHKCDDECMNSVKNGTYDYPKYEEESKLNRNE  172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  


Chain H from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee........eeeeeee.....ee..hhhhhh.....ee...eeeee......eeee.....ee.....eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hf5 H    1 EVQLVESGGGVVQPGRSLRLSCAASGFMFSSYVMHWVRQPPGKGLEWVAVIWYDGSKTYFADSMRGRLTVSRDNSKNALYLQMNRLRAEDTAVYYCARQQDSGYSGPEVSYYSHYGMDVWGQGTMVTVSSASTLVKDYFPEPAVLQSSGLYSL  178
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||||103       113  ||   147||     175   
                                                                              52A                            82A||               100A|||||100J|||             116|    148|           
                                                                                                              82B|                100B|||||100K||              141     167           
                                                                                                               82C                 100C|||||100L|                                    
                                                                                                                                    100D|||||100M                                    
                                                                                                                                     100E||||                                        
                                                                                                                                      100F|||                                        
                                                                                                                                       100G||                                        
                                                                                                                                        100H|                                        
                                                                                                                                         100I                                        


Chain L from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                     
               SCOP domains d4hf5l1 L:3-107 automated matches                                                                              d4hf5l2 L:108-208 automated matches                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eee......eeeeee..........eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeee........eee....eee.......................................ee...ee.....ee..ee.................ee....ee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hf5 L    3 VLTQSPSASGTPGQAITISCSGSSSNIGSNPVNWYQQLPGAAPKLLIYADEHRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLSGPAVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQLVCLISDFYPGAVTVGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                  ||13        23    ||  31        41        51        61        71        81        91    ||||97      106A       116       126|      141    || 162       172       182       192       202      
                                  9|              27A|                                                                  95A|||        106A                 126|           146|                                                  
                                  11               27B                                                                   95B||                              132            158                                                  
                                                                                                                          95C|                                                                                                  
                                                                                                                           95D
   Legend:   → Mismatch (orange background)
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    → 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  (4, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HF5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HF5)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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    Tyr L:140 - Pro L:141   [ RasMol ]  
 
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        C7S226_I57A0 | C7S226: 3ku3 3ku5 3ku6 3qqb 3qqe 3qqi 3qqo 4hlz

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