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(-) Description

Title :  ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS
 
Authors :  R. Mckenna, D. Xia, P. Willingmann, L. L. Ilag, S. Krishnaswamy, M. G. Rossmann, N. H. Olson, T. S. Baker, N. L. Incardona
Date :  03 Dec 91  (Deposition) - 03 Dec 91  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,1,2,3
Biol. Unit 1:  A,1,2,3  (60x)
Keywords :  Protein-Dna Complex, Single Strand, Icosahedral Virus, Virus/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Mckenna, D. Xia, P. Willingmann, L. L. Ilag, S. Krishnaswamy, M. G. Rossmann, N. H. Olson, T. S. Baker, N. L. Incardona
Atomic Structure Of Single-Stranded Dna Bacteriophage Phi X174 And Its Functional Implications.
Nature V. 355 137 1992
PubMed-ID: 1370343  |  Reference-DOI: 10.1038/355137A0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
    Chains: 1
    Engineered: YES
    Expression System: ESCHERICHIA COLI C
    Expression System Strain: C
    Expression System Taxid: 498388
    Organism Scientific: ENTEROBACTERIA PHAGE PHIX174
    Organism Taxid: 10847
 
Molecule 2 - PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
    Chains: 2
    Engineered: YES
    Expression System: ESCHERICHIA COLI C
    Expression System Strain: C
    Expression System Taxid: 498388
    Organism Scientific: ENTEROBACTERIA PHAGE PHIX174
    Organism Taxid: 10847
 
Molecule 3 - PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
    Chains: 3
    Engineered: YES
    Expression System: ESCHERICHIA COLI C
    Expression System Strain: C
    Expression System Taxid: 498388
    Organism Scientific: ENTEROBACTERIA PHAGE PHIX174
    Organism Taxid: 10847
 
Molecule 4 - DNA (5'-D(*AP*AP*AP*AP*C)-3')
    Chains: A
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : A123
Biological Unit 1 (60x): A123

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2BPA)

(-) Sites  (0, 0)

(no "Site" information available for 2BPA)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BPA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BPA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BPA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BPA)

(-) Exons   (0, 0)

(no "Exon" information available for 2BPA)

(-) 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: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 d2bpa1_ 1: Microvirus capsid proteins                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2bpa100 1:1-426 Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeeeeeeeee....eeeeeeeee..eeeeeeeeeeeeeeeee......eeeeeeeeeeee.........hhhhhh........................................hhhhhhhh........................................................hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeeeeeeee..................eeeeeeeeeeeeee.....eeeeeeeeeee.........................hhhhhhh...............................................................hhhhhhh........eeeeeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bpa 1   1 SNIQTGAERMPHDLSHLGFLAGQIGRLITISTTPVIAGDSFEMDAVGALRLSPLRRGLAIDSTVDIFTFYVPHRHVYGEQWIKFMKDGVNATPLPTVNTTGYIDHAAFLGTINPDTNKIPKHLFQGYLNIYNNYFKAPWMPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAYANLHTDQERDYFMQRYRDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS 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 2 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 d2bpa2_ 2: Microvirus capsid proteins                                                                                                                                           SCOP domains
               CATH domains 2bpa200 2:1-175  [code=2.60.120.20, no name defined]                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................eeeeeeeeeee...eeeeeeeeeee...........eeeeeeeeee....eeeeeeeeeeeeee........eeeeeeeeeeeeeeeeeeeee..........eeeeeeeeeeeeee...eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bpa 2   1 MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain 3 from PDB  Type:PROTEIN  Length:36
 aligned with J_BPPHS | P69592 from UniProtKB/Swiss-Prot  Length:38

    Alignment length:36
                                    12        22        32      
              J_BPPHS     3 KGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF  38
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 2bpa 3   2 KGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF  37
                                    11        21        31      


Chain A from PDB  Type:DNA  Length:5
                                     
                 2bpa A   0 AAAAC   4
   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, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BPA)

(-) Gene Ontology  (10, 16)

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

Chain 3   (J_BPPHS | P69592)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_BPPHS | P03641: 1al0 1cd3 1kvp 1phx
        G_BPPHS | P03643: 1al0 1cd3 1phx
        J_BPPHS | P69592: 1rb8

(-) Related Entries Specified in the PDB File

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