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(-) Description

Title :  GPD PRIOR TO CAPSID ASSEMBLY
 
Authors :  M. C. Morais, M. Fisher, K. Kanamaru, B. A. Fane, M. G. Rossmann
Date :  24 Jun 04  (Deposition) - 26 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Scaffolding Protein, Phix174, Assembly, Conformational Switching, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Morais, M. Fisher, S. Kanamaru, L. Przybyla, J. Burgner, B. A. Fane, M. G. Rossmann
Conformational Switching By The Scaffolding Protein D Directs The Assembly Of Bacteriophage Phix174
Mol. Cell V. 15 991 2004
PubMed-ID: 15383287  |  Reference-DOI: 10.1016/J.MOLCEL.2004.08.023
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SCAFFOLDING PROTEIN D
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSE420
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: D
    Organism Scientific: ENTEROBACTERIA PHAGE PHIX174
    Organism Taxid: 10847
    Synonym: GPD

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1TX9)

(-) Sites  (0, 0)

(no "Site" information available for 1TX9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TX9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TX9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TX9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TX9)

(-) Exons   (0, 0)

(no "Exon" information available for 1TX9)

(-) Sequences/Alignments

Asymmetric/Biological 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:141
 aligned with SCAFD_BPPHS | P69486 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:141
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 
          SCAFD_BPPHS     4 VTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQ 144
               SCOP domains ---d1tx9a1 A:7-144 Scaffolding protein gpD of bacteriophage procapsid                                                                         SCOP domains
               CATH domains 1tx9A00 A:4-144 Procapsid Of Bacteriophage Phix174, Chain 1                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tx9 A   4 VTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQ 144
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 


Chain A from PDB  Type:PROTEIN  Length:141
 aligned with SCAFD_BPS13 | P69487 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:141
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 
          SCAFD_BPS13     4 VTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQ 144
               SCOP domains ---d1tx9a1 A:7-144 Scaffolding protein gpD of bacteriophage procapsid                                                                         SCOP domains
               CATH domains 1tx9A00 A:4-144 Procapsid Of Bacteriophage Phix174, Chain 1                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tx9 A   4 VTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQ 144
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 


Chain B from PDB  Type:PROTEIN  Length:130
 aligned with SCAFD_BPPHS | P69486 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:130
                                    15        25        35        45        55        65        75        85        95       105       115       125       135
          SCAFD_BPPHS     6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVL 135
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1tx9B00 B:6-135 Procapsid Of Bacteriophage Phix174, Chain 1                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..hhhhhhhhh.......hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tx9 B   6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVL 135
                                    15        25        35        45        55        65        75        85        95       105       115       125       135


Chain B from PDB  Type:PROTEIN  Length:130
 aligned with SCAFD_BPS13 | P69487 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:130
                                    15        25        35        45        55        65        75        85        95       105       115       125       135
          SCAFD_BPS13     6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVL 135
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1tx9B00 B:6-135 Procapsid Of Bacteriophage Phix174, Chain 1                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..hhhhhhhhh.......hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tx9 B   6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVL 135
                                    15        25        35        45        55        65        75        85        95       105       115       125       135
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1TX9)

(-) Gene Ontology  (3, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SCAFD_BPS13 | P69487)
biological process
    GO:0046797    viral procapsid maturation    The refolding and structural rearrangements of individual capsid subunits to transition from the intermediate procapsid, to the more stable capsid structure.

Chain A,B   (SCAFD_BPPHS | P69486)
biological process
    GO:0046797    viral procapsid maturation    The refolding and structural rearrangements of individual capsid subunits to transition from the intermediate procapsid, to the more stable capsid structure.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SCAFD_BPPHS | P69486: 1al0 1cd3 1m0f

(-) Related Entries Specified in the PDB File

1cd3 SCAFFOLDING PROTEIN GPD ON THE PHIX174 PROCAPSID