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(-) Description

Title :  T=1 CAPSID STRUCTURE OF SESBANIA MOSAIC VIRUS COAT PROTEIN DELETION MUTANT CP-N(DELTA)36
 
Authors :  V. Sangita, G. L. Lokesh, P. S. Satheshkumar, C. S. Vijay, V. Saravanan, H. S. Savithri, M. R. Murthy
Date :  21 Feb 04  (Deposition) - 23 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (60x)
Keywords :  T=1 Capsids, Deletion Mutant, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Sangita, G. L. Lokesh, P. S. Satheshkumar, C. S. Vijay, V. Saravanan, H. S. Savithri, M. R. Murthy
T=1 Capsid Structures Of Sesbania Mosaic Virus Coat Protein Mutants: Determinants Of T=3 And T=1 Capsid Assembly
J. Mol. Biol. V. 342 987 2004
PubMed-ID: 15342251  |  Reference-DOI: 10.1016/J.JMB.2004.07.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET C
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 37-268
    Organism Scientific: SESBANIA MOSAIC VIRUS
    Organism Taxid: 12558

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (60x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:207 , ASN A:267 , ASN A:268BINDING SITE FOR RESIDUE CA A 358

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VB4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VB4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VB4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VB4)

(-) Exons   (0, 0)

(no "Exon" information available for 1VB4)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:196
 aligned with Q9EB06_9VIRU | Q9EB06 from UniProtKB/TrEMBL  Length:268

    Alignment length:196
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262      
         Q9EB06_9VIRU    73 GITVLTHSELSAEIGVTDSIVVSSELVMPYTVGTWLRGVAANWSKYSWLSVRYTYIPSCPSSTAGSIHMGFQYDMADTVPVSVNQLSNLRGYVSGQVWSGSAGLCFINGTRCSDTSTAISTTLDVSKLGKKWYPYKTSADYATAVGVDVNIATPLVPARLVIALLDGSSSTAVAAGRIYCTYTIQMIEPTASALNN 268
               SCOP domains d1vb4a_ A: Sobemovirus coat protein                                                                                                                                                                  SCOP domains
               CATH domains 1vb4A00 A:73-268  [code=2.60.120.20, no name defined]                                                                                                                                                CATH domains
               Pfam domains Viral_coat-1vb4A01 A:73-265                                                                                                                                                                      --- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee....eeeeee.hhhhhhhhhhhhhh.eeeeeeeeeeeeeee........eeeeeee.........hhhhhhhheeeeeee...hhhhhhhhh..........eeee..........ee..hhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeeeeeeeeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vb4 A  73 GITVLTHSELSAEIGVTDSIVVSSELVMPYTVGTWLRGVAANWSKYSWLSVRYTYIPSCPSSTAGSIHMGFQYDMADTVPVSVNQLSNLRGYVSGQVWSGSAGLCFINGTRCSDTSTAISTTLDVSKLGKKWYPYKTSADYATAVGVDVNIATPLVPARLVIALLDGSSSTAVAAGRIYCTYTIQMIEPTASALNN 268
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262
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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  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9EB06_9VIRU | Q9EB06)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.

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  1vb4
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  Q9EB06_9VIRU | Q9EB06
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 Related Entries

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

UniProtKB/TrEMBL
        Q9EB06_9VIRU | Q9EB06: 1smv 1vak 1vb2 1x33 1x35 1x36 2vq0 2wlp 4y4y 4y5z

(-) Related Entries Specified in the PDB File

1smv STRUCTURE OF THE NATIVE VIRUS
1vb2 MUTANT D146N AND D149N