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(-) Description

Title :  THE PHIX174 DNA BINDING PROTEIN J IN TWO DIFFERENT CAPSID ENVIRONMENTS.
 
Authors :  R. A. Bernal, S. Hafenstein, R. Esmeralda, B. A. Fane, M. G. Rossmann
Date :  03 Nov 03  (Deposition) - 13 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  F,G,J,X
Biol. Unit 1:  F,G,J,X  (60x)
Keywords :  Bacteriophage Alpha3, Bacteriophage Phix174, Bacteriophage Alpha3 Chimera, Alpha3, Phix174, Three-Dimentional Structure, Virion, Microviridae, Icosahedral Virus, Virus/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Bernal, S. Hafenstein, R. Esmeralda, B. A. Fane, M. G. Rossmann
The Phix174 Protein J Mediates Dna Packaging And Viral Attachment To Host Cells.
J. Mol. Biol. V. 337 1109 2004
PubMed-ID: 15046981  |  Reference-DOI: 10.1016/J.JMB.2004.02.033
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: F
    Organism Scientific: ENTEROBACTERIA PHAGE ALPHA3
    Organism Taxid: 10849
    Other Details: WT ALPHA3 CAPSID PROTEIN F
    Synonym: F PROTEIN, GPF
 
Molecule 2 - MAJOR SPIKE PROTEIN
    Chains: G
    Organism Scientific: ENTEROBACTERIA PHAGE ALPHA3
    Organism Taxid: 10849
    Other Details: WT ALPHA3 SPIKE PROTEIN G
    Synonym: G PROTEIN, GPG
 
Molecule 3 - SMALL CORE PROTEIN
    Chains: J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: RECA- CELLS
    Expression System Taxid: 562
    Expression System Vector Type: VIRUS
    Gene: J
    Organism Scientific: ENTEROBACTERIA PHAGE PHIX174
    Organism Taxid: 10847
    Synonym: J PROTEIN
 
Molecule 4 - DNA (5'-D(P*CP*AP*AP*A)-3')
    Chains: X
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1DC6Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1DC-1Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL F:13 , ASP F:14 , SER F:16 , GLU F:43 , VAL F:415 , SER F:416 , VAL F:417 , DA X:4BINDING SITE FOR RESIDUE DC X 5
2AC2SOFTWAREPRO F:274 , ARG F:275BINDING SITE FOR RESIDUE DC X 6
3AC3SOFTWAREPHE F:277BINDING SITE FOR RESIDUE DC X 7
4AC4SOFTWAREALA F:38 , GLY F:39 , HIS F:420 , GLN J:36 , DC X:1BINDING SITE FOR RESIDUE DC X 8
5AC5SOFTWARELYS J:21BINDING SITE FOR RESIDUE DC X 10

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RB8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RB8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RB8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RB8)

(-) Exons   (0, 0)

(no "Exon" information available for 1RB8)

(-) 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 F from PDB  Type:PROTEIN  Length:422
 aligned with VGF_BPAL3 | P08767 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:422
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429  
            VGF_BPAL3    10 REIVDLSHLAFDCGMLGRLKTVSWTPVIAGDSFELDAVGALRLSPLRRGLAIDSKVDFFTFYIPHRHVYGDQWIQFMRDGVNAQPLPSVTCNRYPDHAGYVGTIVPANNRIPKFLHQSYLNIYNNYFRAPWMPERTEANPSNLNEDDARYRFRCCHLKNIWSAPLPPETKLAEEMGIESNSIDIMGLQAAYAQLHTEQERTYFMQRYRDVISSFGGSTSYDADNRPLLVMHTDFWASGYDVDGTDQSSLGQFSGRVQQTFKHSVPRFFVPEHGVMMTLALIRFPPISPLEHHYLAGKSQLTYTDLAGDPALIGNLPPREISYRDLFRDGRSGIKIKVAESIWYRTHPDYVNFKYHDLHGFPFLDDAPGTSTGDNLQEAILVRHQDYDACFQSQQLLQWNKQARYNVSVYRHMPTVRDSIMTS 431
               SCOP domains d1rb8f_ F: Microvirus capsid proteins                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1rb8F00 F:10-431 Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1                                                                                                                                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Phage_F-1rb8F01 F:187-429                                                                                                                                                                                                                          -- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Phage_F-1rb8F02 F:187-429                                                                                                                                                                                                                          -- Pfam domains (2)
         Sec.struct. author .eeee..eeeeeee.....eeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeehhhhhhhhhhhhhhhhhhh....eee.......hhhhh.......eeehhhhhhhhhhhhhhh................hhhhhhhh...............................hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...........eeeeeeeeee.eeeee.........eeeeeeeeeeeeeeeee....eeeeeeeeee.........hhhhhh...hhhhhh.hhhhhh....eeee.hhh........eeee..hhhhh......hhhhhhh................hhhhhhh..hhhhhh.........eeeeeeeeeeeee...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rb8 F  10 REIVDLSHLAFDCGMLGRLKTVSWTPVIAGDSFELDAVGALRLSPLRRGLAIDSKVDFFTFYIPHRHVYGDQWIQFMRDGVNAQPLPSVTCNRYPDHAGYVGTIVPANNRIPKFLHQSYLNIYNNYFRAPWMPERTEANPSNLNEDDARYGFRCCHLKNIWSAPLPPETKLAEEMGIESNSIDIMGLQAAYAQLHTEQERTYFMQRYRDVISSFGGSTSYDADNRPLLVMHTDFWASGYDVDGTDQSSLGQFSGRVQQTFKHSVPRFFVPEHGVMMTLALIRFPPISPLEHHYLAGKSQLTYTDLAGDPALIGNLPPREISYRDLFRDGRSGIKIKVAESIWYRTHPDYVNFKYHDLHGFPFLDDAPGTSTGDNLQEAILVRHQDYDACFQSQQLLQWNKQARYNVSVYRHMPTVRDSIMTS 431
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429  


Chain G from PDB  Type:PROTEIN  Length:187
 aligned with G_BPAL3 | P31281 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
              G_BPAL3     1 MYQNFVTKHDTAIQTSRFSVTGNVIPAAPTGNIPVINGGSITAERAVVNLYANMNVSTSSDGSFIVAMKVDTSPTDPNCVISAGVNLSFAGTSYPIVGIVRFESASEQPTSIAGSEVEHYPIEMSVGSGGVCSARDCATVDIHPRTSGNNVFVGVICSSAKWTSGRVIGTIATTQVIHEYQVLQPLK 187
               SCOP domains d1rb8g_ G: Microvirus capsid proteins                                                                                                                                                       SCOP domains
               CATH domains 1rb8G00 G:1-187  [code=2.60.120.20, no name defined]                                                                                                                                        CATH domains
               Pfam domains Phage_G-1rb8G01 G:1-187                                                                                                                                                                     Pfam domains
         Sec.struct. author ................eeeeeeee.......eee..........eeeeeeeeee.......eeeeeeee........eeeeeeeeeeee......eeeeeeeee......eee.hhheee.....ee...eeeeeeeeeee........eeeeeeeeee.....eeeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rb8 G   1 MYQNFVTKHDTAIQTSRFSVTGNVIPAAPTGNIPVINGGSITAERAVVNLYANMNVSTSSDGSFIVAMKVDTSPTDPNCVISAGVNLSFAGTSYPIVGIVRFESASEQPTSIAGSEVEHYPIEMSVGSGGVCSARDCATVDIHPRTSGNNVFVGVICSSAKWTSGRVIGTIATTQVIHEYQVLQPLK 187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       


Chain J from PDB  Type:PROTEIN  Length:26
 aligned with J_BPPHS | P69592 from UniProtKB/Swiss-Prot  Length:38

    Alignment length:29
                                    19        29         
              J_BPPHS    10 ARPGRPQPLRGTKGKRKGARLWYVGGQQF  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
                 1rb8 J   9 ARPGRPQPLRGTK---KGARLWYVGGQQF  37
                                    18  |   | 28         
                                       21  25            


Chain X from PDB  Type:DNA  Length:10
                                          
                 1rb8 X   1 CAAACCCCCC  10
                                    10
   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  (2, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Phage_F] (2)
(-)
Clan: no clan defined [family: Phage_G] (2)

(-) Gene Ontology  (9, 13)

Asymmetric Unit(hide GO term definitions)
Chain F   (VGF_BPAL3 | P08767)
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: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_BPAL3 | P31281)
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: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 J   (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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  VGF_BPAL3 | P08767
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 Related Entries

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

UniProtKB/Swiss-Prot
        G_BPAL3 | P31281: 1m06 1m0f
        J_BPPHS | P69592: 2bpa
        VGF_BPAL3 | P08767: 1m06 1m0f

(-) Related Entries Specified in the PDB File

1m06 WILD TYPE ALPHA3 VIRION
1m0f WILD TYPE ALPHA3 PROCAPSID
2bpa WILD TYPE PHIX174 VIRION