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(-) Description

Title :  RECOMBINANT T=3 CAPSID OF A SITE SPECIFIC MUTANT OF SEMV CP
 
Authors :  V. Sangita, G. L. Lokesh, P. S. Satheshkumar, V. Saravanan, C. S. Vijay, H. S. Savithri, M. R. Murthy
Date :  29 Apr 05  (Deposition) - 18 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  T=3 Capsids, Beta-Annulus, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Sangita, G. L. Lokesh, P. S. Satheshkumar, V. Saravanan, C. S. Vijay, H. S. Savithri, M. R. Murthy
Structural Studies On Recombinant T = 3 Capsids Of Sesbania Mosaic Virus Coat Protein Mutants.
Acta Crystallogr. , Sect. D V. 61 1402 2005
PubMed-ID: 16204893  |  Reference-DOI: 10.1107/S0907444905024029
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: SESBANIA MOSAIC VIRUS
    Organism Taxid: 12558

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (60x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:146 , ASP A:149 , TYR B:207 , ASN B:267 , ASN B:268BINDING SITE FOR RESIDUE CA A 269
2AC2SOFTWAREASP B:146 , ASP B:149 , TYR C:207 , ASN C:267 , ASN C:268BINDING SITE FOR RESIDUE CA C 270
3AC3SOFTWARETYR A:207 , ASN A:267 , ASN A:268 , ASP C:146 , ASP C:149BINDING SITE FOR RESIDUE CA A 271

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:177 -A:184
2C:177 -C:184

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X35)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X35)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X35)

(-) Exons   (0, 0)

(no "Exon" information available for 1X35)

(-) 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: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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeee....eeeeee.hhhhhhhhhhhhhh.eeeeeeeeeeeeeee........eeeeeee.........hhhhhhhheeeeeee...hhhhhhhhh...........eeeehhhhh....ee..hhhhhhhhhh.hhhhh......eeeeeee.......eeeeeeeeeeeeeeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x35 A  73 GITVLTHSELSAEIGVTDSIVVSSELVMPYTVGTWLRGVAANWSKYSWLSVRYTYIPSCPSSTAGSIHMGFQYDMADTVPVSVNQLSNLRGYVSGQVWSGSAGLCFINGTRCSDTSTAISTTLDVSKLGKKWYPYKTSADYATAVGVDVNIATPLVPARLVIALLDGSSSTAVAAGRIYCTYTIQMIEPTASALNN 268
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262      


Chain B from PDB  Type:PROTEIN  Length:197
 aligned with Q9EB06_9VIRU | Q9EB06 from UniProtKB/TrEMBL  Length:268

    Alignment length:197
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       
         Q9EB06_9VIRU    72 GGITVLTHSELSAEIGVTDSIVVSSELVMPYTVGTWLRGVAANWSKYSWLSVRYTYIPSCPSSTAGSIHMGFQYDMADTVPVSVNQLSNLRGYVSGQVWSGSAGLCFINGTRCSDTSTAISTTLDVSKLGKKWYPYKTSADYATAVGVDVNIATPLVPARLVIALLDGSSSTAVAAGRIYCTYTIQMIEPTASALNN 268
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee.....eeeeee.hhhhhhhhhhhhhh.eeeeeeee.eeeeee........eeeeeee.........hhhhhh..eeeeeee...hhhhhhhh............eee.hhhhh....ee..hhhhhhhhhhhhhhhhh.....eeeeeee........eeeeeeeeeeeeeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x35 B  72 GGITVLTHSELSAEIGVTDSIVVSSELVMPYTVGTWLRGVAANWSKYSWLSVRYTYIPSCPSSTAGSIHMGFQYDMADTVPVSVNQLSNLRGYVSGQVWSGSAGLCFINGTRCSDTSTAISTTLDVSKLGKKWYPYKTSADYATAVGVDVNIATPLVPARLVIALLDGSSSTAVAAGRIYCTYTIQMIEPTASALNN 268
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       


Chain C from PDB  Type:PROTEIN  Length:225
 aligned with Q9EB06_9VIRU | Q9EB06 from UniProtKB/TrEMBL  Length:268

    Alignment length:225
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263     
         Q9EB06_9VIRU    44 PTQAGISMAPSAQGAMVRIRNPAVSSSRGGITVLTHSELSAEIGVTDSIVVSSELVMPYTVGTWLRGVAANWSKYSWLSVRYTYIPSCPSSTAGSIHMGFQYDMADTVPVSVNQLSNLRGYVSGQVWSGSAGLCFINGTRCSDTSTAISTTLDVSKLGKKWYPYKTSADYATAVGVDVNIATPLVPARLVIALLDGSSSTAVAAGRIYCTYTIQMIEPTASALNN 268
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Viral_coat-1x35C01 C:46-265                                                                                                                                                                                                 --- Pfam domains (1)
           Pfam domains (2) --Viral_coat-1x35C02 C:46-265                                                                                                                                                                                                 --- Pfam domains (2)
           Pfam domains (3) --Viral_coat-1x35C03 C:46-265                                                                                                                                                                                                 --- Pfam domains (3)
         Sec.struct. author ......................eeee.....eeeeeeeeeeeeee....eeeeee.hhhhhhhhhhhhhh.eeeeeeeeeeeeeee........eeeeeee.........hhhhhhhheeeeeee...hhhhhhhhh...........eee.hhhhh....ee..hhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeeeeeeeeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x35 C  44 PTQAGISMAASAQGAMVRIRNPAVSSSRGGITVLTHSELSAEIGVTDSIVVSSELVMPYTVGTWLRGVAANWSKYSWLSVRYTYIPSCPSSTAGSIHMGFQYDMADTVPVSVNQLSNLRGYVSGQVWSGSAGLCFINGTRCSDTSTAISTTLDVSKLGKKWYPYKTSADYATAVGVDVNIATPLVPARLVIALLDGSSSTAVAAGRIYCTYTIQMIEPTASALNN 268
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
   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 1X35)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X35)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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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  1x35
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 Related Entries

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

UniProtKB/TrEMBL
        Q9EB06_9VIRU | Q9EB06: 1smv 1vak 1vb2 1vb4 1x33 1x36 2vq0 2wlp 4y4y 4y5z

(-) Related Entries Specified in the PDB File

1smv 1x33 1x34 1x36