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(-) Description

Title :  STRUCTURAL BASIS FOR IMMUNIZATION WITH POST-FUSION RSV F TO ELICIT HIGH NEUTRALIZING ANTIBODY TITERS
 
Authors :  K. A. Swanson, E. C. Settembre, C. A. Shaw, A. K. Dey, R. Rappuoli, C. W. Ma P. D. Dormitzer, A. Carfi
Date :  18 Apr 11  (Deposition) - 18 May 11  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Fusion Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Swanson, E. C. Settembre, C. A. Shaw, A. K. Dey, R. Rappuoli, C. W. Mandl, P. R. Dormitzer, A. Carfi
Structural Basis For Immunization With Postfusion Respiratory Syncytial Virus Fusion F Glycoprotein (Rsv F) T Elicit High Neutralizing Antibody Titers.
Proc. Natl. Acad. Sci. Usa V. 108 9619 2011
PubMed-ID: 21586636  |  Reference-DOI: 10.1073/PNAS.1106536108

(-) Compounds

Molecule 1 - FUSION GLYCOPROTEIN F0
    Chains: A, B, C
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: RESPIRATORY SYNCYTIAL VIRUS F, RESIDUES 1-524
    Gene: F
    Organism Scientific: HUMAN RESPIRATORY SYNCYTIAL VIRUS
    Organism Taxid: 11250
    Other Details: FUSION PEPTIDE DELETED
    Synonym: PROTEIN F, FUSION GLYCOPROTEIN F2, FUSION GLYCOPROTEIN F1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 13)

Asymmetric/Biological Unit (1, 13)
No.NameCountTypeFull Name
1NAG13Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS B:68 , ASN B:70 , NAG B:1536BINDING SITE FOR RESIDUE NAG B 1535
02AC2SOFTWARENAG B:1535BINDING SITE FOR RESIDUE NAG B 1536
03AC3SOFTWAREASN C:496 , ASN C:500 , NAG C:1546BINDING SITE FOR RESIDUE NAG C 1545
04AC4SOFTWARENAG C:1545BINDING SITE FOR RESIDUE NAG C 1546
05AC5SOFTWARELYS C:68 , ASN C:70 , NAG C:1536BINDING SITE FOR RESIDUE NAG C 1535
06AC6SOFTWARENAG C:1535BINDING SITE FOR RESIDUE NAG C 1536
07AC7SOFTWAREASN A:496 , ASN A:500 , NAG A:1546BINDING SITE FOR RESIDUE NAG A 1545
08AC8SOFTWARENAG A:1545BINDING SITE FOR RESIDUE NAG A 1546
09AC9SOFTWAREASN A:27BINDING SITE FOR RESIDUE NAG A 1525
10BC1SOFTWAREASN A:70 , NAG A:1536BINDING SITE FOR RESIDUE NAG A 1535
11BC2SOFTWARENAG A:1535BINDING SITE FOR RESIDUE NAG A 1536
12BC3SOFTWARESER B:493 , ASN B:496 , ASN B:500 , NAG B:1546BINDING SITE FOR RESIDUE NAG B 1545
13BC4SOFTWARENAG B:1545BINDING SITE FOR RESIDUE NAG B 1546

(-) SS Bonds  (21, 21)

Asymmetric/Biological Unit
No.Residues
1A:37 -A:439
2A:69 -A:212
3A:313 -A:343
4A:322 -A:333
5A:358 -A:367
6A:382 -A:393
7A:416 -A:422
8B:37 -B:439
9B:69 -B:212
10B:313 -B:343
11B:322 -B:333
12B:358 -B:367
13B:382 -B:393
14B:416 -B:422
15C:37 -C:439
16C:69 -C:212
17C:313 -C:343
18C:322 -C:333
19C:358 -C:367
20C:382 -C:393
21C:416 -C:422

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RKI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 9)

Asymmetric/Biological Unit (3, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_FUS_HRSVA_002 *E218AFUS_HRSVA  ---  ---A/B/CE218A
2UniProtVAR_FUS_HRSVA_003 *I379VFUS_HRSVA  ---  ---A/B/CV379V
3UniProtVAR_FUS_HRSVA_004 *M447VFUS_HRSVA  ---  ---A/B/CV447V
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RKI)

(-) Sequences/Alignments

Asymmetric/Biological 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:441
 aligned with FUS_HRSVA | P03420 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:492
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515  
            FUS_HRSVA    26 QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPPTNNRARRELPRFMNYTLNNAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEINLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGMDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLHNVN 517
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhh........................................hhhhhhhhhhhhhhhhhhhhhh-----------------------------------------------.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh........................................----........................hhh.............hhh...hhhhhhhhh...................................................................................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------------------------------------------------------V-------------------------------------------------------------------V---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rki A  26 QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQ-----------------------------------------------SAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTN----SNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLHNVN 517
                                    35        45        55        65        75        85        95  |      -         -         -         -         -|      155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325    |  335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515  
                                                                                                   98                                             146                                                                                                                                                                                325  330                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:439
 aligned with FUS_HRSVA | P03420 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:492
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515  
            FUS_HRSVA    26 QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPPTNNRARRELPRFMNYTLNNAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEINLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGMDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLHNVN 517
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhh........................................hhhhhhhhhhhhhhhhhhhhhh-------------------------------------------------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........................................----........................hhhhh...........hhh...hhhhhhhhh...................................................................................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------------------------------------------------------V-------------------------------------------------------------------V---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rki B  26 QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQ-------------------------------------------------IASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTN----SNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLHNVN 517
                                    35        45        55        65        75        85        95  |      -         -         -         -         -  |    155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325    |  335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515  
                                                                                                   98                                               148                                                                                                                                                                              325  330                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:439
 aligned with FUS_HRSVA | P03420 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:492
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515  
            FUS_HRSVA    26 QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPPTNNRARRELPRFMNYTLNNAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEINLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGMDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLHNVN 517
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --Fusion_gly-3rkiC01 C:28-517                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) --Fusion_gly-3rkiC02 C:28-517                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Pfam domains (2)
           Pfam domains (3) --Fusion_gly-3rkiC03 C:28-517                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Pfam domains (3)
         Sec.struct. author ........hhh........................................hhhhhhhhhhhhhhhhhhhh..-----------------------------------------------------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....................................................................hhh.............hhh...hhhhhhhhh...................................................................................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------------------------------------------------------V-------------------------------------------------------------------V---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rki C  26 QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQ-----------------------------------------------------VAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLHNVN 517
                                    35        45        55        65        75        85        95  |      -         -         -         -         -      |155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515  
                                                                                                   98                                                   152
   Legend:   → Mismatch (orange background)
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  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 3RKI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RKI)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Fusion_gly] (9)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (FUS_HRSVA | P03420)
biological process
    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:0006948    induction by virus of host cell-cell fusion    The process of syncytia-forming cell-cell fusion, caused by a virus.
    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:0060141    positive regulation of syncytium formation by virus    The process in which a virus increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
    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.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        FUS_HRSVA | P03420: 2mdp 3ixt 3kpe 3o41 3o45 3rrr 3rrt 4ccf 4jhw 4mmq 4mmr 4mms 4mmt 4mmu 4mmv 4zyp 5c69 5c6b 5ea3 5ea4 5ea5 5ea6 5ea7 5ea8 5j3d 5k6b 5k6c 5k6f 5k6g 5k6h 5k6i 5toj 5tok 5tpn 5u68 5udc

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