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(-) Description

Title :  ELECTRON CRYO-MICROSCOPY OF COWPEA MOSAIC VIRUS CONTAINING RNA-1 (CPMVB)
 
Authors :  E. L. Hesketh, Y. Meshcheriakova, K. C. Dent, P. Saxena, R. Thompson, J. J. Cockburn, G. P. Lomonossoff, N. A. Ranson
Date :  27 May 15  (Deposition) - 23 Dec 15  (Release) - 19 Apr 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.44
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (60x)
Keywords :  Virus, Cpmv, Comoviridae, Picornavirales. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. L. Hesketh, Y. Meshcheriakova, K. C. Dent, P. Saxena, R. F. Thompson J. J. Cockburn, G. P. Lomonossoff, N. A. Ranson
Mechanisms Of Assembly And Genome Packaging In An Rna Virus Revealed By High-Resolution Cryo-Em.
Nat Commun V. 6 10113 2015
PubMed-ID: 26657148  |  Reference-DOI: 10.1038/NCOMMS10113

(-) Compounds

Molecule 1 - RNA2 POLYPROTEIN
    Chains: A
    Fragment: LARGE COAT PROTEIN
    Organism Common: CPMV
    Organism Scientific: COWPEA MOSAIC VIRUS
    Organism Taxid: 12264
    Other Details: WILD-TYPE VIRUS CONTAINING RNA-1
    Synonym: GENOME POLYPROTEIN M, P2, COAT PROTEIN VP37, COAT PROTEIN VP23, COWPEA MOSAIC VIRUS
 
Molecule 2 - RNA2 POLYPROTEIN
    Chains: B
    Fragment: SMALL COAT PROTEIN N-TERMINUS PART
    Organism Common: CPMV
    Organism Scientific: COWPEA MOSAIC VIRUS
    Organism Taxid: 12264
    Other Details: WILD-TYPE VIRUS CONTAINING RNA-1
    Synonym: GENOME POLYPROTEIN M, P2, COAT PROTEIN VP37, COAT PROTEIN VP23, COWPEA MOSAIC VIRUS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (60x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5A32)

(-) Sites  (0, 0)

(no "Site" information available for 5A32)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A32)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:1 -Pro A:2
2Ala A:22 -Pro A:23
3Arg A:77 -Gly A:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A32)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A32)

(-) Exons   (0, 0)

(no "Exon" information available for 5A32)

(-) 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:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeee.........eeeeee....eeee......eeee..hhhhhhhhheeeeeeeeeeeeeee....hhhhh...eeeeee........eeeeeee.....eeeeeeeee.......ee...hhhhh...eeeeee.......eeeeeeee....eeeeeee...ee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a32 A   1 GPVCAEASDVYSPCMIASTPPAPFSDVTAVTFDLINGKITPVGDDNWNTHIYNPPIMNVLRTAAWKSGTIHVQLNVRGAGVKRADWDGQVFVYLRQSMNPESYDARTFVISQPGSAMLNFSFDIIGPNSGFEFAESPWANQTTWYLECVATNPRQIQQFEVNMRFDPNFRVAGNILMPPFPLSTETPPL 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain B from PDB  Type:PROTEIN  Length:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.................eeeeeee.......eeeeeee.hhhhh.....hhhhhhhh....eeeeeee..........eeeeeee.ee......hhhhhhh.eeeee.......eeeee.........hhhhhhhh..eeeeeeee.........eeeeeeeeeeeee.....ee...eeeeeeeeeeeeeeee.......eeeee......ee...eee.hhhhhhhh...eeeeeeeeeeee........eeeeeeee........hhhhh..eeee......ee..eehhhhh...ee..............eeeeeee...........eeeeeeeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a32 B   1 MEQNLFALSLDDTSSVRGSLLDTKFAQTRVLLSKAMAGGDVLLDEYLYDVVNGQDFRATVAFLRTHVITGKIKVTATTNISDNSGCCLMLAINSGVRGKYSTDVYTICSQDSMTWNPGCKKNFSFTFNPNPCGDSWSAEMISRSRVRMTVICVSGWTLSPTTDVIAKLDWSIVNEKCEPTIYHLADCQNWLPLNRWMGKLTFPQGVTSEVRRMPLSIGGGAGATQAFLANMPNSWISMWRYFRGELHFEVTKMSSPYIKATVTFLIAFGNLSDAFGFYESFPHRIVQFAEVEEKCTLVFSQQEFVTAWSTQVNPRTTLEADGCPYLYAIIHDSTTGTISGDFNLGVKLVGIKDFCGIGSNPGIDGSRL 368
                                    10        20        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
   Legend:   → Mismatch (orange background)
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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 5A32)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A32)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A32)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:22 - Pro A:23   [ RasMol ]  
    Arg A:77 - Gly A:78   [ RasMol ]  
    Gly A:1 - Pro A:2   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        POL2_CPMVS | P03599: 1ny7 2bfu 5a33 5fmo

(-) Related Entries Specified in the PDB File

5a33 ELECTRON CRYO-MICROSCOPY OF COWPEA MOSAIC VIRUS (CPMV) EMPTY VIRUS LIKE PARTICLE (EVLP)