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(-) Description

Title :  NOVEL INTER-SUBUNIT CONTACTS IN BARLEY STRIPE MOSAIC VIRUS REVEALED BY CRYO-EM
 
Authors :  D. K. Clare, E. Pechnikova, E. Skurat, V. Makarov, O. S. Sokolova, A. G. S E. V Orlova
Date :  03 Jul 15  (Deposition) - 02 Sep 15  (Release) - 21 Oct 15  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.10
Chains :  Asym. Unit :  A,R
Biol. Unit 1:  A,R  (111x)
Keywords :  Bsmv, Virus, Helical, Cryo-Em, Image Processing, Msa (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. K. Clare, E. V. Pechnikova, E. V. Skurat, V. V. Makarov, O. S. Sokolova, A. G. Solovyev, E. V. Orlova
Novel Inter-Subunit Contacts In Barley Stripe Mosaic Virus Revealed By Cryo-Electron Microscopy.
Structure V. 23 1815 2015
PubMed-ID: 26278173  |  Reference-DOI: 10.1016/J.STR.2015.06.028

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Atcc: PV-328
    Chains: A
    Engineered: YES
    Expression System: AGROBACTERIUM TUMEFACIENS
    Expression System Strain: GV3101
    Expression System Taxid: 358
    Organism Scientific: BARLEY STRIPE MOSAIC VIRUS
    Organism Taxid: 12327
    Other Details: ONLY CONTAINS RESIDUES 3-131 AND 147-194 IN STRUCTURE
    Other Details - Source: PURIFIED FROM NICOTIANA BENTHAMIANA INFECTED PLANTS
    Synonym: BETA-A PROTEIN, COAT PROTEIN
 
Molecule 2 - RNA
    Chains: R
    Organism Scientific: TOBACCO MOSAIC VIRUS (STRAIN OM)
    Organism Taxid: 12251

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AR
Biological Unit 1 (111x): AR

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5A79)

(-) Sites  (0, 0)

(no "Site" information available for 5A79)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A79)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:12 -His A:13
2Arg A:47 -Gly A:48
3Phe A:51 -Ser A:52
4Leu A:67 -Asp A:68
5Val A:75 -Asp A:76
6Gly A:81 -Ala A:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A79)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A79)

(-) Exons   (0, 0)

(no "Exon" information available for 5A79)

(-) 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:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhh...........ee..hhhhhhhhh..........hhhhhhhhh...............................ee..hhhhhhhhhhhhhhh....hhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eehhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a79 A   3 NVSLTAKGGGHYIEDQWDTQVVEAGVFDDWWVHVEAWNKFLDNLRGINFSVASSRSQVAEYLAALDRDLPADVDRRFAGARGQIGSPNYLPAPKFFRLDKRTIAELTRLSRLTDQPHNNRDIELNRAKRLTLRDVQPLKDSALHYQYVLIDLQSARLPVYTRKTFERELALEWIIPD 194
                                    12        22        32        42        52        62        72        82        92       102       112       122       147       157       167       177       187       
                                                                                                                                                          131|                                               
                                                                                                                                                           147                                               


Chain R from PDB  Type:RNA  Length:3
                                   
                 5a79 R   1 GAA   3
   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 5A79)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A79)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A79)

(-) Gene Ontology  (4, 4)

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  Cis Peptide Bonds
    Arg A:47 - Gly A:48   [ RasMol ]  
    Gly A:12 - His A:13   [ RasMol ]  
    Gly A:81 - Ala A:82   [ RasMol ]  
    Leu A:67 - Asp A:68   [ RasMol ]  
    Phe A:51 - Ser A:52   [ RasMol ]  
    Val A:75 - Asp A:76   [ RasMol ]  
 
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  5a79
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_BSMV | P04866: 5a7a

(-) Related Entries Specified in the PDB File

5a7a NOVEL INTER-SUBUNIT CONTACTS IN BARLEY STRIPE MOSAIC VIRUS REVEALED BY CRYO-EM