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(-) Description

Title :  STRUCTURE OF THE PARAINFLUENZA VIRUS 5 F PROTEIN IN ITS METASTABLE, PRE-FUSION CONFORMATION
 
Authors :  H. -S. Yin, X. Wen, R. G. Paterson, R. A. Lamb, T. S. Jardetzky
Date :  11 Oct 05  (Deposition) - 24 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Fusion Protein, Pre-Fusion Conformation, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. -S. Yin, X. Wen, R. G. Paterson, R. A. Lamb, T. S. Jardetzky
Structure Of The Parainfluenza Virus 5 F Protein In Its Metastable, Prefusion Conformation
Nature V. 439 38 2006
PubMed-ID: 16397490  |  Reference-DOI: 10.1038/NATURE04322

(-) Compounds

Molecule 1 - FUSION GLYCOPROTEIN F0
    Chains: A, B, C
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PMELBAC
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: RESIDUES 20-477
    Gene: F
    Organism Scientific: SIMIAN VIRUS 5
    Organism Taxid: 11207

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:65 , THR A:67BINDING SITE FOR RESIDUE NAG A 1065
02AC2SOFTWAREMET A:54 , ASN A:73 , THR A:265 , HOH A:1481BINDING SITE FOR RESIDUE NAG A 1073
03AC3SOFTWAREASN A:352 , THR A:354BINDING SITE FOR RESIDUE NAG A 1352
04AC4SOFTWAREASN A:457BINDING SITE FOR RESIDUE NAG A 1457
05AC5SOFTWAREASN B:65 , HOH B:1463 , HOH B:1478BINDING SITE FOR RESIDUE NAG B 1065
06AC6SOFTWAREASN B:73 , GLN B:145 , THR B:265 , TYR B:266 , MET B:267BINDING SITE FOR RESIDUE NAG B 1073
07AC7SOFTWAREASN B:352 , THR B:354 , HOH B:1468BINDING SITE FOR RESIDUE NAG B 1352
08AC8SOFTWAREASN B:457BINDING SITE FOR RESIDUE NAG B 1457
09AC9SOFTWAREASN C:65 , THR C:67 , SER C:70BINDING SITE FOR RESIDUE NAG C 1065
10BC1SOFTWAREASN C:73 , THR C:265 , TYR C:266BINDING SITE FOR RESIDUE NAG C 1073
11BC2SOFTWAREASN C:352 , THR C:354BINDING SITE FOR RESIDUE NAG C 1352
12BC3SOFTWAREASN C:457 , SER C:461BINDING SITE FOR RESIDUE NAG C 1457

(-) SS Bonds  (15, 15)

Asymmetric/Biological Unit
No.Residues
1A:64 -A:185
2A:324 -A:333
3A:348 -A:356
4A:380 -A:385
5A:387 -A:410
6B:64 -B:185
7B:324 -B:333
8B:348 -B:356
9B:380 -B:385
10B:387 -B:410
11C:64 -C:185
12C:324 -C:333
13C:348 -C:356
14C:380 -C:385
15C:387 -C:410

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B9B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B9B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B9B)

(-) Exons   (0, 0)

(no "Exon" information available for 2B9B)

(-) 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:478
 aligned with FUS_PIV5 | P04849 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:485
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500     
             FUS_PIV5    21 DPAALMQIGVIPTNVRQLMYYTEASSAFIVVKLMPTIDSPISGCNITSISSYNATVTKLLQPIGENLETIRNQLIPTRRRRRFAGVVIGLAALGVATAAQVTAAVALVKANENAAAILNLKNAIQKTNAAVADVVQATQSLGTAVQAVQDHINSVVSPAITAANCKAQDAIIGSILNLYLTELTTIFHNQITNPALSPITIQALRILLGSTLPTVVEKSFNTQISAAELLSSGLLTGQIVGLDLTYMQMVIKIELPTLTVQPATQIIDLATISAFINNQEVMAQLPTRVMVTGSLIQAYPASQCTITPNTVYCRYNDAQVLSDDTMACLQGNLTRCTFSPVVGSFLTRFVLFDGIVYANCRSMLCKCMQPAAVILQPSSSPVTVIDMYKCVSLQLDNLRFTITQLANVTYNSTIKLESSQILSIDPLDISQNLAAVNKSLSDALQHLAQSDTYLSAITSATTTSVLSIIAICLGSLGLILIILLS 505
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2b9bA04 A:443-504                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeeeeeeeeeeeeeeeeeeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--.........hhhhh.eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.......hhhhh..hhhhhhhhhh.hhhhhhhhhh....hhhhhhhh...eeeeeeee....eeeeeeeeeeeeeeeeeeeeeeee..eee..eeeee....eeeee..eeee...........ee.......ee.hhhhhhhhh.hhhhh.eee...hhhh.eeee..eeee......eee.....ee........eee.......eee..eee........----............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b9b A  21 DPAALMQIGVIPTNVRQLMYYTEASSAFIVVKLMPTIDSPISGCNITSISSYNATVTKLLQPIGENLETIRNQLIPT--RRRFAGVVIGLAALGVATAAQVTAAVALVKANENAAAILNLKNAIQKTNAAVADVVQATQSLGTAVQAVQDHINSVVSPAITAANCKAQDAIIGSILNLYLTELTTIFHNQITNPALSPITIQALRILLGSTLPTVVEKSFNTQISAAELLSSGLLTGQIVGLDLTYMQMVIKIELPTLTVQPATQIIDLATISAFINNQEVMAQLPTRVMVTGSLIQAYPASQCTITPNTVYCRYNDAQVLSDDTMACLQGNLTRCTFSPVVGSFLTRFVLFDGIVYANCRSMLCKCMQPAAVILQPSSSPVTVIDMYKCVSLQLDNLRFTITQLANV----TIKLESSQILSIDPLDISQNLAAVNKSLSDALQHLAQSDTYLSAIEDK-IEEILSKIYHIENEIARIKKLIGE 504
                                    30        40        50        60        70        80        90      |100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       | -  |    440       450       460       470       480 |     489       499     
                                                                                                       97  |                                                                                                                                                                                                                                                                                                                                     428  433                                            480 |                       
                                                                                                         100                                                                                                                                                                                                                                                                                                                                                                                           481                       


Chain B from PDB  Type:PROTEIN  Length:482
 aligned with FUS_PIV5 | P04849 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:485
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499     
             FUS_PIV5    20 LDPAALMQIGVIPTNVRQLMYYTEASSAFIVVKLMPTIDSPISGCNITSISSYNATVTKLLQPIGENLETIRNQLIPTRRRRRFAGVVIGLAALGVATAAQVTAAVALVKANENAAAILNLKNAIQKTNAAVADVVQATQSLGTAVQAVQDHINSVVSPAITAANCKAQDAIIGSILNLYLTELTTIFHNQITNPALSPITIQALRILLGSTLPTVVEKSFNTQISAAELLSSGLLTGQIVGLDLTYMQMVIKIELPTLTVQPATQIIDLATISAFINNQEVMAQLPTRVMVTGSLIQAYPASQCTITPNTVYCRYNDAQVLSDDTMACLQGNLTRCTFSPVVGSFLTRFVLFDGIVYANCRSMLCKCMQPAAVILQPSSSPVTVIDMYKCVSLQLDNLRFTITQLANVTYNSTIKLESSQILSIDPLDISQNLAAVNKSLSDALQHLAQSDTYLSAITSATTTSVLSIIAICLGSLGLILIILL 504
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2b9bB04 B:443-503                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhh.eeeeeeeee.....eeeeeeeee.............hhhhhhhhhhhh..hhhhhhhhhhhhh.....--.........hhhhh.eeehhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...eeeee....eeeeee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..hhhhhhhhhh.hhhhhhhhh.....hhhhhhhh...eeeeeeee....eeeeeeeee........eeeeeee..eee..eeeee....eeeee..eeee...........ee.......ee.hhhhhhhhh.hhhhh.eee...hhhh.eeee..eeee......eee....eee........eee......eeee..eeee.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-h.hhhh..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b9b B  20 LDPAALMQIGVIPTNVRQLMYYTEASSAFIVVKLMPTIDSPISGCNITSISSYNATVTKLLQPIGENLETIRNQLIPT--RRRFAGVVIGLAALGVATAAQVTAAVALVKANENAAAILNLKNAIQKTNAAVADVVQATQSLGTAVQAVQDHINSVVSPAITAANCKAQDAIIGSILNLYLTELTTIFHNQITNPALSPITIQALRILLGSTLPTVVEKSFNTQISAAELLSSGLLTGQIVGLDLTYMQMVIKIELPTLTVQPATQIIDLATISAFINNQEVMAQLPTRVMVTGSLIQAYPASQCTITPNTVYCRYNDAQVLSDDTMACLQGNLTRCTFSPVVGSFLTRFVLFDGIVYANCRSMLCKCMQPAAVILQPSSSPVTVIDMYKCVSLQLDNLRFTITQLANVTYNSTIKLESSQILSIDPLDISQNLAAVNKSLSDALQHLAQSDTYLSAIEDK-IEEILSKIYHIENEIARIKKLIG 503
                                    29        39        49        59        69        79        89       | -|      109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479| |    488       498     
                                                                                                        97  |                                                                                                                                                                                                                                                                                                                                                                                         480 |                      
                                                                                                          100                                                                                                                                                                                                                                                                                                                                                                                           481                      


Chain C from PDB  Type:PROTEIN  Length:481
 aligned with FUS_PIV5 | P04849 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:484
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499    
             FUS_PIV5    20 LDPAALMQIGVIPTNVRQLMYYTEASSAFIVVKLMPTIDSPISGCNITSISSYNATVTKLLQPIGENLETIRNQLIPTRRRRRFAGVVIGLAALGVATAAQVTAAVALVKANENAAAILNLKNAIQKTNAAVADVVQATQSLGTAVQAVQDHINSVVSPAITAANCKAQDAIIGSILNLYLTELTTIFHNQITNPALSPITIQALRILLGSTLPTVVEKSFNTQISAAELLSSGLLTGQIVGLDLTYMQMVIKIELPTLTVQPATQIIDLATISAFINNQEVMAQLPTRVMVTGSLIQAYPASQCTITPNTVYCRYNDAQVLSDDTMACLQGNLTRCTFSPVVGSFLTRFVLFDGIVYANCRSMLCKCMQPAAVILQPSSSPVTVIDMYKCVSLQLDNLRFTITQLANVTYNSTIKLESSQILSIDPLDISQNLAAVNKSLSDALQHLAQSDTYLSAITSATTTSVLSIIAICLGSLGLILIIL 503
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2b9bC04 C:443-502 Classic Zinc Finger                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhh.eeeeeeeee....eeeeeeeeee........ee...hhhhhhhhhhhh..hhhhhhhhhhhh......--.........hhhhh.eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....eeeeee..hhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhhhhhhh.hhhhhhhhhh....hhhhhhhh...eeeeeeee....eeeeeeeeee.......eeeeeee..eee..eeeee....eeeee..eeee...........ee..........hhhhhhhhh.hhhhh.eee...hhhh.eeee..eeee.......ee....ee.........eee......eee....eee.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-hhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b9b C  20 LDPAALMQIGVIPTNVRQLMYYTEASSAFIVVKLMPTIDSPISGCNITSISSYNATVTKLLQPIGENLETIRNQLIPT--RRRFAGVVIGLAALGVATAAQVTAAVALVKANENAAAILNLKNAIQKTNAAVADVVQATQSLGTAVQAVQDHINSVVSPAITAANCKAQDAIIGSILNLYLTELTTIFHNQITNPALSPITIQALRILLGSTLPTVVEKSFNTQISAAELLSSGLLTGQIVGLDLTYMQMVIKIELPTLTVQPATQIIDLATISAFINNQEVMAQLPTRVMVTGSLIQAYPASQCTITPNTVYCRYNDAQVLSDDTMACLQGNLTRCTFSPVVGSFLTRFVLFDGIVYANCRSMLCKCMQPAAVILQPSSSPVTVIDMYKCVSLQLDNLRFTITQLANVTYNSTIKLESSQILSIDPLDISQNLAAVNKSLSDALQHLAQSDTYLSAIEDK-IEEILSKIYHIENEIARIKKLI 502
                                    29        39        49        59        69        79        89       | -|      109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479| |    488       498    
                                                                                                        97  |                                                                                                                                                                                                                                                                                                                                                                                         480 |                     
                                                                                                          100                                                                                                                                                                                                                                                                                                                                                                                           481
   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 2B9B)

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B9B)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (FUS_PIV5 | P04849)
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:0046761    viral budding from plasma membrane    A viral budding that starts with formation of a membrane curvature in the host plasma membrane.
    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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  2b9b
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 Related Entries

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

UniProtKB/Swiss-Prot
        FUS_PIV5 | P04849: 1svf 4gip 4wsg

(-) Related Entries Specified in the PDB File

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