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(-) Description

Title :  CRYSTAL STRUCTURE OF A GENERATION 4 INFLUENZA HEMAGGLUTININ STABILIZED STEM IN COMPLEX WITH THE BROADLY NEUTRALIZING ANTIBODY CR6261
 
Authors :  J. C. Boyington, P. D. Kwong, G. J. Nabel, J. R. Mascola
Date :  12 Jun 15  (Deposition) - 02 Sep 15  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.30
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: HEK293 GNTI-/-
    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
    Other Details: ENGINEERED FUSION BETWEEN AN INFLUENZA HEMAGGLUTININ STEM, AN HIV-1 GP41 SIX-HELIX BUNDLE AND T4 PHAGE FOLDON
    Strain: A/NEW CALEDONIA/20/1999(H1N1), ISOLATE HXB2
    Synonym: ENV POLYPROTEIN,ENV POLYPROTEIN
 
Molecule 2 - CR6261 ANTIBODY HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - CR6261 ANTIBODY LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5C0S)

(-) Sites  (0, 0)

(no "Site" information available for 5C0S)

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:4 -A:219
2A:226 -A:230
3H:22 -H:92
4H:140 -H:196
5L:23 -L:88
6L:139 -L:198

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly H:27 -Pro H:28
2Pro H:41 -Gly H:42
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Tyr L:145 -Pro L:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C0S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C0S)

(-) Exons   (0, 0)

(no "Exon" information available for 5C0S)

(-) 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:242
                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eee.......eee..eee.....eee.........................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5c0s A    1 DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLGSGLRMVTGLRNIPQAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMGGDPEWDREINNYTSIIYSLIEESQNQQEIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCNNECMESVKNGTYDYPKYSEESKLNREKI  255
                                    10        20        30        40      ||55        65        75        85        95       105       115       125       135||     153       163       173       183       193       203       213       223       233       243       253  
                                                                         47|                                                                                136|                                                                                                              
                                                                          53                                                                                 145                                                                                                              


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee.....eeeeeee.........eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5c0s H    1 EVQLVESGAEVKKPGSSVKVSCKASGGPFRSYAISWVRQAPGQGPEWMGGIIPIFGTTKYAPKFQGRVTITADDFAGTVYMELSSLRSEDTAMYYCAKHMGYQVRETMDVWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122       132       142       152       162       172       182       192       202       212 
                                                                              52A                            82A||               100A|||                                                                                                                 
                                                                                                              82B|                100B||                                                                                                                 
                                                                                                               82C                 100C|                                                                                                                 
                                                                                                                                    100D                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....eeeeee....hhhhh..eeeee......eeee.............eeeeee..eeeeee.........eeeeeeee.....eeee...eeeee.......eeeee..hhhhhh...eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5c0s L    3 VLTQPPSVSAAPGQKVTISCSGSSSNIGNDYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEANYYCATWDRRPTAYVVFGGGTKLTVLQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE  215
                                  ||13        23    ||  31        41        51        61        71        81        91    ||| 98       113       123       133       143       153       163       173       183       193       203       213  
                                  9|              27A|                                                                  95A||         107|                                                                                                      
                                  11               27B                                                                   95B|          113                                                                                                      
                                                                                                                          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  (0, 0)

(no "SCOP Domain" information available for 5C0S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C0S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C0S)

(-) Gene Ontology  (34, 49)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Gly H:27 - Pro H:28   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Pro H:41 - Gly H:42   [ RasMol ]  
    Tyr L:145 - Pro L:146   [ RasMol ]  
 
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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 5c0r 5cil 5cin 5cmu 5cmz 5cn0 5dd0 5ghw 5h0n 5hfl 5hm1 5ivx 5ka5 5ka6 5x08
UniProtKB/TrEMBL
        D9IEJ2_BPT4 | D9IEJ2: 4zyp 5c0r
        Q6WG00_9INFA | Q6WG00: 5c0r

(-) Related Entries Specified in the PDB File

3gbm H5N1 HEMAGGLUTININ COMPLEX WITH CR6261 FAB
3gbn H1N1 HEMAGGLUTININ COMPLEX WITH CR6261 FAB
4evn UNLIGANDED CR6261
5c0r