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(-) Description

Title :  CRYSTAL STRUCTURE OF A GENERATION 3 INFLUENZA HEMAGGLUTININ STABILIZED STEM COMPLEXED WITH THE BROADLY NEUTRALIZING ANTIBODY C179
 
Authors :  J. C. Boyington, P. D. Kwong, G. J. Nabel, J. R. Mascola
Date :  12 Jun 15  (Deposition) - 02 Sep 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.19
Chains :  Asym. Unit :  A,H,L
Biol. Unit 1:  A,H,L  (3x)
Keywords :  Hemagglutinin, Immunogen, Trimer, Complex, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. M. Yassine, J. C. Boyington, P. M. Mctamney, C. J. Wei, M. Kanekiyo, W. P. Kong, J. R. Gallagher, L. Wang, Y. Zhang, M. G. Joyce, D. Lingwood, S. M. Moin, H. Andersen, Y. Okuno, S. S. Rao, A. K. Harris, P. D. Kwong, J. R. Mascola, G. J. Nabel, B. S. Graham
Hemagglutinin-Stem Nanoparticles Generate Heterosubtypic Influenza Protection.
Nat. Med. V. 21 1065 2015
PubMed-ID: 26301691  |  Reference-DOI: 10.1038/NM.3927

(-) Compounds

Molecule 1 - HEMAGGLUTININ, ENVELOPE GLYCOPROTEIN, FIBRITIN FUSION PROTEIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: UNP Q6WG00 RESIDUES 18-49, 328-402, 436-517, UNP P04578 RESIDUES 546-577, 628-654 AND UNP D9IEJ2 RESIDUES 458-485
    Gene: HA, ENV, WAC
    Organism Scientific: INFLUENZA A VIRUS, HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SUBTYPE B, ENTEROBACTERIA PHAGE T4
    Organism Taxid: 381512, 11706, 10665
    Strain: A/NEW CALEDONIA/20/1999(H1N1), ISOLATE HXB2
 
Molecule 2 - C179 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - C179 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : AHL
Biological Unit 1 (3x): AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:115 , ASN A:119 , TYR A:120binding site for Mono-Saccharide NAG A 401 bound to ASN A 119
2AC2SOFTWAREGLU A:229 , GLU A:232 , ASN A:236 , THR A:238binding site for Poly-Saccharide residues NAG A 402 through NAG A 403 bound to ASN A 236

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:4 -A:219
2A:226 -A:230
3H:22 -H:92
4H:140 -H:195
5L:23 -L:88
6L:134 -L:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Thr L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149
6Trp H:188 -Pro H:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C0R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C0R)

(-) Exons   (0, 0)

(no "Exon" information available for 5C0R)

(-) 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:270
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......eee.......eee..eee.....eee.........................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh.......hhhhhhhhhhhh............eeee..eeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5c0r A    1 DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLGWGLRMVTGLRNIPQAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMGGWMEWDREINNYTSIIYSLIEESQNQQENGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCNNECMESVKNGTYDYPKYSEESKLNREKIGYIPEAPRDGQAYVRKDGEWVLLSTF  285
                                    10        20        30        40      ||55        65        75        85        95       105       115       125       135  ||   151       161       171       181       191       201       211       221       231       241       251   ||  265       275       285
                                                                         47|                                                                                  138|                                                                                                           255|                         
                                                                          53                                                                                   145                                                                                                            260                         


Chain H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee..eee....eeeeeee..........eeeeee......eeeeee.hhhhh..eee.......eeeee.....eeeeeee..hhhhheeeeeee..........ee...eeeee........eeee...........eeee.eeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5c0r H    1 EVKLVESGGGLVQPGGSLRLSCGTSGFTLTDDYMTWVRQPPGKALEWLGFIRDRANGYTTEYSASVKGRFTISRDNSQSIVYLQMNTLRVEDSATYYCARPKGYFPYAMDYWGQGTSVIVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      |101       111       121       131       141       151       161       171       181       191       201       211  
                                                                              52A||                            82A||               100A||                                                                                                                 
                                                                               52B|                             82B|                100B|                                                                                                                 
                                                                                52C                              82C                 100C                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....ee.eeee.......eeeeee.......eeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..........eeeeeeeeeee....eeeeeee..eee.....eee.........eeeee.eeeehhhhhhh.eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5c0r L    1 DIQMTQSPASQSASLGESVTITCLASQTIGTWLAWYQQKPGKSPQLLIYAATSLADGVPSRFSGSGSGTKFSFKISSLQAEDFVSYYCQQLYSTPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (0, 0)

(no "SCOP Domain" information available for 5C0R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C0R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C0R)

(-) Gene Ontology  (34, 49)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        D9IEJ2_BPT4 | D9IEJ2: 4ncu 4ncv 4ncw
        ENV_HV1H2 | P04578: 1aik 1df4 1df5 1dlb 1g9m 1gc1 1gzl 1k33 1k34 1mzi 1opn 1opt 1opw 1rzj 2cmr 2me1 2mg1 2mg2 2mg3 2ny7 2pv6 2x7r 2xra 2zzo 3d0v 3dnl 3dnn 3dno 3dro 3idx 3idy 3j70 3tyg 3vie 4jpj 4jpk 4ydv 4zto 5bn0 5c0s 5cil 5cin 5cmu 5cmz 5cn0 5dd0 5ghw 5h0n 5hfl 5hm1 5ivx 5ka5 5ka6 5x08
UniProtKB/TrEMBL
        D9IEJ2_BPT4 | D9IEJ2: 4zyp 5c0s
        Q6WG00_9INFA | Q6WG00: 5c0s

(-) Related Entries Specified in the PDB File

4hlz COMPLEX OF STEM ANTIBODY C179 WITH AN H2N2 HEMAGGLUTININ TRIMER
5c0s