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(-) Description

Title :  CRYSTAL STRUCTURE OF THE AUTHENTIC FLOCK HOUSE VIRUS PARTICLE
 
Authors :  J. A. Speir, Z. Chen, V. S. Reddy, J. E. Johnson
Date :  27 Jun 12  (Deposition) - 01 Aug 12  (Release) - 01 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,R
Biol. Unit 1:  A,B,C,D,E,F,R  (60x)
Keywords :  Virus, Flock House Virus, Nodavirus, Rna, Beta-Barrel, Jellyroll, Aspartyl Protease, Capsid Protein, Hydrolase, Autoproteolysis, Virion, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Speir, Z. Chen, V. S. Reddy, J. E. Johnson
Structural Study Of Virus Assembly Intermediates Reveals Maturation Event Sequence And A Staging Position For Externalized Lytic Peptides
To Be Published 2012
PubMed: search

(-) Compounds

Molecule 1 - CAPSID PROTEIN BETA
    Chains: A, B, C
    EC Number: 3.4.23.44
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell Line: DL-1
    Gene: ALPHA, COAT PROTEIN ALPHA
    Organism Common: FHV
    Organism Scientific: FLOCK HOUSE VIRUS
    Organism Taxid: 12287
    Synonym: COAT PROTEIN BETA
 
Molecule 2 - CAPSID PROTEIN GAMMA
    Chains: D, E, F
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell Line: DL-1
    Gene: ALPHA, COAT PROTEIN ALPHA
    Organism Common: FHV
    Organism Scientific: FLOCK HOUSE VIRUS
    Organism Taxid: 12287
    Synonym: PEPTIDE GAMMA, COAT PROTEIN GAMMA
 
Molecule 3 - FLOCK HOUSE VIRUS GENOMIC RNA
    Chains: R
    Organism Scientific: FLOCK HOUSE VIRUS
    Organism Taxid: 12287
    Other Details: GENOMIC RNA PRODUCED DURING VIRUS REPLICATION IN DL-1 CELLS.

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFR
Biological Unit 1 (60x): ABCDEFR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Biological Unit 1 (1, 180)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3EPE180Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:157 , ASP A:161 , GLU A:257 , ASP C:221 , GLY C:273 , HOH C:516BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREASP A:221 , GLY A:273 , ASP B:161BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREASP A:249 , GLU A:251 , ASP B:249 , ASP C:249 , GLU C:251BINDING SITE FOR RESIDUE CA A 403
4AC4SOFTWAREGLY A:258 , GLN A:260 , PRO A:264 , ALA A:265 , GLU A:283 , HOH A:546 , GLN C:201 , PHE C:202 , PRO C:203BINDING SITE FOR RESIDUE EPE A 404
5AC5SOFTWAREASP B:221 , GLY B:273 , ASP C:161BINDING SITE FOR RESIDUE CA B 401
6AC6SOFTWARESER B:102BINDING SITE FOR RESIDUE CL B 402
7AC7SOFTWAREGLN A:201 , PHE A:202 , PRO A:203 , GLY B:258 , ILE B:259 , GLN B:260 , ALA B:265 , GLU B:283 , HOH B:544BINDING SITE FOR RESIDUE EPE B 403
8AC8SOFTWAREGLN B:201 , PHE B:202 , PRO B:203 , GLY C:258 , GLN C:260 , ALA C:265 , ALA C:282 , GLU C:283 , HOH C:524BINDING SITE FOR RESIDUE EPE C 401

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:69 -A:318
2B:69 -B:318
3C:69 -C:318

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asp A:207 -Pro A:208
2Leu A:262 -Pro A:263
3Asp B:207 -Pro B:208
4Leu B:262 -Pro B:263
5Asp C:207 -Pro C:208
6Leu C:262 -Pro C:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FTB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FTB)

(-) Exons   (0, 0)

(no "Exon" information available for 4FTB)

(-) 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:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhh..................eeeeeeeeeeeeeee...eeeeeee.....eeeeeeeee.........eeeeee..hhhhhhh.........eeeeeeeeeeeeeee.........eeeeeee..eeeeeeeee.....eeeeeeeeehhhhhhh....eeeee.hhheeee..........ee......ee.....hhhhhh...eee................eeeeeee......eeeeeeeeeeeeeee....hhhhhhee....hhhhhhhhhhhhhhh..eehhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ftb A  20 TQTAPVPQQNVPRLTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVSRKDVLNQSISFTAGQDTFILIAPTPGVAYWSASVPAGTFPTSATTFNPVNYPGFTSMFGTTSTSRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLDGVLAVGPDNFSESFIKGVFSQSACNEPDFEFNDILEGIQTLPPANVSLGSTGQPFTMDSGAEATSGVVGWGNMDTIVIRVSAPEGAVNSAILKAWSCIEYRPNPNAMLYQFGHDSPPLDEVALQEYRTVARSLPVAVIAAQN 363
                                    29  ||    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362 
                                       32|                                                                                                                                                                                                                                                                                                                   
                                        56                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh..................eeeeeeeeeeeeeee...eeeeeee.....eeeeeeeee.........eeeeee..hhhhhhh.........eeeeeeeeeeeeeee.........eeeeeee..eeeeeeeee.....eeeeeeeeehhhhhhh.....eeee.hhheeeee.........ee......ee.....hhhhhh...eee................eeeeeee......eeeeeeeeeeeeeee...hhhhhhhee....hhhhhhhhhhhhhhh..ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ftb B  53 MAALTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVSRKDVLNQSISFTAGQDTFILIAPTPGVAYWSASVPAGTFPTSATTFNPVNYPGFTSMFGTTSTSRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLDGVLAVGPDNFSESFIKGVFSQSACNEPDFEFNDILEGIQTLPPANVSLGSTGQPFTMDSGAEATSGVVGWGNMDTIVIRVSAPEGAVNSAILKAWSCIEYRPNPNAMLYQFGHDSPPLDEVALQEYRTVARSLPVAVIAAQN 363
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362 


Chain C from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh..............eeeeeeeeeeeeeee...eeeeeee.....eeeeeeeee.........eeeeee..hhhhhhh.........eeeeeeeeeeeeeee.........eeeeeee..eeeeeeeee.....eeeeeeeeehhhhhhh.....eeee.hhheeeee.........ee......ee..............eee................eeeeeee......eeeeeeeeeeeeeee...hhhhhhhee....hhhhhhhhhhhhhhh..eehhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ftb C  55 ALTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVSRKDVLNQSISFTAGQDTFILIAPTPGVAYWSASVPAGTFPTSATTFNPVNYPGFTSMFGTTSTSRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLDGVLAVGPDNFSESFIKGVFSQSACNEPDFEFNDILEGIQTLPPANVSLGSTGQPFTMDSGAEATSGVVGWGNMDTIVIRVSAPEGAVNSAILKAWSCIEYRPNPNAMLYQFGHDSPPLDEVALQEYRTVARSLPVAVIAAQN 363
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354         


Chain D from PDB  Type:PROTEIN  Length:21
                                                     
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 4ftb D 364 ASMWERVKSIIKSSLAAASNI 384
                                   373       383 


Chain E from PDB  Type:PROTEIN  Length:19
                                                   
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 4ftb E 364 ASMWERVKSIIKSSLAAAS 382
                                   373         


Chain F from PDB  Type:PROTEIN  Length:20
                                                    
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 4ftb F 364 ASMWERVKSIIKSSLAAASN 383
                                   373       383


Chain R from PDB  Type:RNA  Length:15
                                               
                 4ftb R   1 UUUCUCUUUUAUCUU  15
                                    10
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4FTB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FTB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FTB)

(-) Gene Ontology  (10, 10)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_FHV | P12870: 3lob 4fsj 4fte 4fts

(-) Related Entries Specified in the PDB File

1f8v PARIACOTO VIRUS (PAV)
1nov NODAMURA VIRUS (NOV)
2bbv BLACK BEETLE VIRUS (BBV)
3lob FHV CALCIUM DEFICIENT MUTANT
4fsj
4fte
4fts