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(-) Description

Title :  PROCAPSID OF BACTERIOPHAGE PHIX174
 
Authors :  M. G. Rossmann, T. Dokland
Date :  05 Mar 99  (Deposition) - 14 Apr 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  B,F,G,1,2,3,4
Biol. Unit 1:  B,F,G,1,2,3,4  (60x)
Keywords :  Complex (Virus Capsid Proteins), Bacteriophage, Procapsid, Scaffolding Protein, Chaperone, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Dokland, R. A. Bernal, A. Burch, S. Pletnev, B. A. Fane, M. G. Rossmann
The Role Of Scaffolding Proteins In The Assembly Of The Small, Single-Stranded Dna Virus Phix174.
J. Mol. Biol. V. 288 595 1999
PubMed-ID: 10329166  |  Reference-DOI: 10.1006/JMBI.1999.2699
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (SCAFFOLDING PROTEIN GPD)
    Chains: 1, 2, 3, 4
    Organism Scientific: ENTEROBACTERIA PHAGE PHIX174
    Organism Taxid: 10847
    Strain: C
 
Molecule 2 - PROTEIN (CAPSID PROTEIN GPF)
    Chains: F
    Organism Scientific: ENTEROBACTERIA PHAGE PHIX174
    Organism Taxid: 10847
    Strain: C
 
Molecule 3 - PROTEIN (SPIKE PROTEIN GPG)
    Chains: G
    Organism Scientific: ENTEROBACTERIA PHAGE PHIX174
    Organism Taxid: 10847
    Strain: C
 
Molecule 4 - PROTEIN (SCAFFOLDING PROTEIN GPB)
    Chains: B
    Organism Scientific: ENTEROBACTERIA PHAGE PHIX174
    Organism Taxid: 10847
    Strain: C

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : BFG1234
Biological Unit 1 (60x): BFG1234

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1CD3)

(-) Sites  (0, 0)

(no "Site" information available for 1CD3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CD3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CD3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CD3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CD3)

(-) Exons   (0, 0)

(no "Exon" information available for 1CD3)

(-) 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 1 from PDB  Type:PROTEIN  Length:143
 aligned with SCAFD_BPPHS | P69486 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:143
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145   
          SCAFD_BPPHS     6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRA 148
               SCOP domains d1cd31_ 1: Scaffolding protein gpD of bacteriophage procapsid                                                                                   SCOP domains
               CATH domains 1cd3100 1:6-148 Procapsid Of Bacteriophage Phix174, Chain 1                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.......hhhhhhh.......hhhhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhh......hhhhhhh.....hhhhhh.......hhhhhhhhhhhhhh.........hhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cd3 1   6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRA 148
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145   


Chain 2 from PDB  Type:PROTEIN  Length:135
 aligned with SCAFD_BPPHS | P69486 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:135
                                    15        25        35        45        55        65        75        85        95       105       115       125       135     
          SCAFD_BPPHS     6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEE 140
               SCOP domains d1cd32_ 2: Scaffolding protein gpD of bacteriophage procapsid                                                                           SCOP domains
               CATH domains 1cd3200 2:6-140 Procapsid Of Bacteriophage Phix174, Chain 1                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.hhhhhhhhhhhhh......hhhhhhhh.........hhhhhhhhhhhhhhhhhhh........hhhhhhhhhh...hhhhhhhhhhh....................hhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cd3 2   6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEE 140
                                    15        25        35        45        55        65        75        85        95       105       115       125       135     


Chain 3 from PDB  Type:PROTEIN  Length:140
 aligned with SCAFD_BPPHS | P69486 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:140
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144
          SCAFD_BPPHS     5 TEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQ 144
               SCOP domains d1cd33_ 3: Scaffolding protein gpD of bacteriophage procapsid                                                                                SCOP domains
               CATH domains 1cd3300 3:5-144 Procapsid Of Bacteriophage Phix174, Chain 1                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.......hhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..hhhhhhhhhhh.....hhhhhh.......hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cd3 3   5 TEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQ 144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144


Chain 4 from PDB  Type:PROTEIN  Length:146
 aligned with SCAFD_BPPHS | P69486 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:146
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146      
          SCAFD_BPPHS     7 QSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM 152
               SCOP domains d1cd34_ 4: Scaffolding protein gpD of bacteriophage procapsid                                                                                      SCOP domains
               CATH domains 1cd3400 4:7-152 Procapsid Of Bacteriophage Phix174, Chain 1                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh..........hhhhhhh..........hhhhhhhhhhhhhhhhhhh........hhhhhhhhhh......hhhhhhhh..................hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cd3 4   7 QSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM 152
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146      


Chain B from PDB  Type:PROTEIN  Length:68
 aligned with SCAFB_BPPHS | P03633 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:120
                                    10        20        30        40        50        60        70        80        90       100       110       120
          SCAFB_BPPHS     1 MEQLTKNQAVATSQEAVQNQNEPQLRDENAHNDKSVHGVLNPTYQAGLRRDAVQPDIEAERKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDKNDWRIQPAEFYRFHDAEVNTFGYF 120
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........----------------------------------------------------.hhhhhhh..................hhhhhh...................hhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cd3 B   1 MEQLTKNQ----------------------------------------------------RKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDKNDWRIQPAEFYRFHDAEVNTFGYF 120
                                   | -         -         -         -         -         -|       70        80        90       100       110       120
                                   8                                                   61                                                           


Chain F from PDB  Type:PROTEIN  Length:426
 aligned with CAPSD_BPPHS | P03641 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:426
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421      
          CAPSD_BPPHS     2 SNIQTGAERMPHDLSHLGFLAGQIGRLITISTTPVIAGDSFEMDAVGALRLSPLRRGLAIDSTVDIFTFYVPHRHVYGEQWIKFMKDGVNATPLPTVNTTGYIDHAAFLGTINPDTNKIPKHLFQGYLNIYNNYFKAPWMPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAYANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS 427
               SCOP domains d1cd3f_ F: Microvirus capsid proteins                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1cd3F00 F:1-426 Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee..eeeeeee.........eeee......eeeeeeee............eeeee..eeeehhhh....hhhhhhhhhh.....eee........hhh........eeehhhhhhhhhhhhhh.............hhh..hhhhh..................................hhhhhhhhhhhhhhhhhhh....hhhhhhhh.................eeeee......................eeeeee........eeee..eeeee.........hhhh.....hhhh...hhhhh....eeeehhh.........eeee...hhh.......................................hhh........eeeeeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cd3 F   1 SNIQTGAERMPHDLSHLGFLAGQIGRLITISTTPVIAGDSFEMDAVGALRLSPLRRGLAIDSTVDIFTFYVPHRHVYGEQWIKFMKDGVNATPLPTVNTTGYIDHAAFLGTINPDTNKIPKHLFQGYLNIYNNYFKAPWMPDRTEANPNELNQDDARFGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAYANLHTDQERDYFMQRYRDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS 426
                                    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       370       380       390       400       410       420      


Chain G from PDB  Type:PROTEIN  Length:175
 aligned with G_BPPHS | P03643 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
              G_BPPHS     1 MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK 175
               SCOP domains d1cd3g_ G: Microvirus capsid proteins                                                                                                                                           SCOP domains
               CATH domains 1cd3G00 G:1-175  [code=2.60.120.20, no name defined]                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee.....................eeeeee..eee..eeeeeeeeee........eeee..eeeeee......eeeeeeeee...........eee....eee..eeeee..eeee........eeeeeeeeeeee..eeeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cd3 G   1 MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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  (2, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CD3)

(-) Gene Ontology  (13, 19)

Asymmetric Unit(hide GO term definitions)
Chain 1,2,3,4   (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.

Chain B   (SCAFB_BPPHS | P03633)
biological process
    GO:0019069    viral capsid assembly    The assembly of a virus capsid from its protein subunits.
    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.
    GO:0046729    viral procapsid    A stable empty viral capsid produced during the assembly of viruses.

Chain F   (CAPSD_BPPHS | P03641)
molecular function
    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:0039615    T=1 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=1 symmetry. The T=1 capsid is composed of 12 pentameric capsomeres.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    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.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

Chain G   (G_BPPHS | P03643)
biological process
    GO:0019048    modulation by virus of host morphology or physiology    The process in which a virus effects a change in the structure or processes of its host organism.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    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.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  1cd3
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  G_BPPHS | P03643
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  SCAFB_BPPHS | P03633
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  SCAFD_BPPHS | P69486
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_BPPHS | P03641: 1al0 1kvp 1phx 2bpa
        G_BPPHS | P03643: 1al0 1phx 2bpa
        SCAFB_BPPHS | P03633: 1al0
        SCAFD_BPPHS | P69486: 1al0 1m0f 1tx9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1CD3)