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(-) Description

Title :  SOLUTION STRUCTURE OF THE RESPIRATORY SYNCYTIAL VIRUS (RSV)SIX-HELIX BUNDLE COMPLEXED WITH TMC353121, A SMALL-MOLEUCULE INHIBITOR OF RSV
 
Authors :  D. Roymans, H. De Bondt, E. Arnoult, M. D. Cummings, H. Van Vlijmen, K.
Date :  16 Nov 09  (Deposition) - 22 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Peptide-Small-Molecule Complex, Alpha Helix, Coiled-Coil, Envelope Protein, Fusion Protein, Glycoprotein, Host Cell Membrane, Host Membrane, Lipoprotein, Membrane, Palmitate, Transmembrane, Virion, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Roymans, H. L. De Bondt, E. Arnoult, P. Geluykens, T. Gevers, M. Van Ginderen, N. Verheyen, H. Kim, R. Willebrords, J. F. Bonfanti, W. Bruinzeel, M. D. Cummings, H. Van Vlijmen, K. Andries
Binding Of A Potent Small-Molecule Inhibitor Of Six-Helix Bundle Formation Requires Interactions With Both Heptad-Repeats Of The Rsv Fusion Protein.
Proc. Natl. Acad. Sci. Usa V. 107 308 2010
PubMed-ID: 19966279  |  Reference-DOI: 10.1073/PNAS.0910108106

(-) Compounds

Molecule 1 - FUSION GLYCOPROTEIN F0
    Chains: A
    Fragment: PROTEINASE K-RESISTANT CORE OF HEPTAD REPEAT 1
    Organism Scientific: HUMAN RESPIRATORY SYNCYTIAL VIRUS
    Organism Taxid: 11259
    Strain: A2
    Synonym: PROTEIN F, FUSION GLYCOPROTEIN F2, FUSION GLYCOPROTEIN F1
 
Molecule 2 - FUSION GLYCOPROTEIN F0
    Chains: B
    Fragment: PROTEINASE K-RESISTANT CORE OF HEPTAD REPEAT 2
    Organism Scientific: HUMAN RESPIRATORY SYNCYTIAL VIRUS
    Organism Taxid: 11259
    Strain: A2
    Synonym: PROTEIN F, FUSION GLYCOPROTEIN F2, FUSION GLYCOPROTEIN F1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL
2TM31Ligand/Ion2-[[6-[[[2-(3-HYDROXYPROPYL)-5-METHYLPHENYL]AMINO]METHYL]-2-[[3-(4-MORPHOLINYL)PROPYL]AMINO]-1H-BENZIMIDAZOL-1-YL]METHYL]-6-METHYL-3-PYRIDINOL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1PG43Ligand/IonTETRAETHYLENE GLYCOL
2TM33Ligand/Ion2-[[6-[[[2-(3-HYDROXYPROPYL)-5-METHYLPHENYL]AMINO]METHYL]-2-[[3-(4-MORPHOLINYL)PROPYL]AMINO]-1H-BENZIMIDAZOL-1-YL]METHYL]-6-METHYL-3-PYRIDINOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:196 , TYR A:198 , ASP A:200 , LYS A:201 , GLN A:202 , PG4 A:210 , HOH A:211 , HOH B:7 , SER B:485 , ASP B:486 , PHE B:488 , ARG B:507 , GLU B:511BINDING SITE FOR RESIDUE TM3 A 1
2AC2SOFTWARETM3 A:1 , SER A:173 , TYR A:198 , ASP A:200 , GLN A:202 , LYS B:508BINDING SITE FOR RESIDUE PG4 A 210

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KPE)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe B:483 -Pro B:484

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KPE)

(-) 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:49
 aligned with FUS_HRSVA | P03420 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:49
                                   168       178       188       198         
            FUS_HRSVA   159 HLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIV 207
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains 3kpeA00 A:159-207                                 CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 3kpe A 159 HLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIV 207
                                   168       178       188       198         


Chain B from PDB  Type:PROTEIN  Length:35
 aligned with FUS_HRSVA | P03420 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:35
                                   492       502       512     
            FUS_HRSVA   483 FPSDEFDASISQVNEKINQSLAFIRKSDELLHNVN 517
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
           Pfam domains (1) Fusion_gly-3kpeB01 B:483-517        Pfam domains (1)
           Pfam domains (2) Fusion_gly-3kpeB02 B:483-517        Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 3kpe B 483 FPSDEFDASISQVNEKINQSLAFIRKSDELLHNVN 517
                                   492       502       512
   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 3KPE)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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

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UniProtKB/Swiss-Prot
        FUS_HRSVA | P03420: 2mdp 3ixt 3o41 3o45 3rki 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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