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(-) Description

Title :  STRUCTURAL STUDIES OF BACTERIOPHAGE ALPHA3 ASSEMBLY, X-RAY CRYSTALLOGRAPHY
 
Authors :  R. A. Bernal, S. Hafenstein, N. H. Olson, V. Bowman, P. R. Chipman, T. S. B B. A. Fane, M. G. Rossmann
Date :  12 Jun 02  (Deposition) - 25 Dec 02  (Release) - 28 Dec 11  (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, Three-Dimensional Structure, Virion, Morphogenesis, Phix174, Assembly, Microviridae, Icosahedral Virus, Virus-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Bernal, S. Hafenstein, N. H. Olson, V. Bowman, P. R. Chipman, T. S. Baker, B. A. Fane, M. G. Rossmann
Structural Studies Of Bacteriophage Alpha3 Assembly
J. Mol. Biol. V. 325 11 2003
PubMed-ID: 12473449  |  Reference-DOI: 10.1016/S0022-2836(02)01201-9

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ENTEROBACTERIA PHAGE ALPHA3
    Organism Taxid: 10849
    Synonym: F PROTEIN, GPF
 
Molecule 2 - MAJOR SPIKE PROTEIN
    Chains: G
    Engineered: YES
    Organism Scientific: ENTEROBACTERIA PHAGE ALPHA3
    Organism Taxid: 10849
    Synonym: G PROTEIN, GPG
 
Molecule 3 - SMALL CORE PROTEIN
    Chains: J
    Engineered: YES
    Organism Scientific: ENTEROBACTERIA PHAGE ALPHA3
    Organism Taxid: 10849
    Synonym: J PROTEIN
 
Molecule 4 - 5'-D(P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR) P*(3DR)P*(3DR)P*(3DR))-3'
    Chains: X
    Engineered: YES
    Organism Scientific: ENTEROBACTERIA PHAGE ALPHA3
    Organism Taxid: 10849
    Other Details: SSDNA FRAGMENT

 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, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
13DR10OTHER1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
Biological Unit 1 (1, 600)
No.NameCountTypeFull Name
13DR600OTHER1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE F:212 , ASP F:218 , ARG J:15 , SER J:22 , 3DR X:2 , 3DR X:3 , 3DR X:7BINDING SITE FOR RESIDUE 3DR X 1
02AC2SOFTWARELYS F:167 , GLN J:23 , PHE J:24 , 3DR X:1 , 3DR X:3BINDING SITE FOR RESIDUE 3DR X 2
03AC3SOFTWARELYS F:167 , LEU J:16 , TRP J:17 , 3DR X:1 , 3DR X:2 , 3DR X:4BINDING SITE FOR RESIDUE 3DR X 3
04AC4SOFTWAREARG J:11 , GLY J:13 , ALA J:14 , LEU J:16 , TRP J:17 , 3DR X:3BINDING SITE FOR RESIDUE 3DR X 4
05AC5SOFTWAREARG F:217 , SER F:221 , ARG F:234 , SER J:22BINDING SITE FOR RESIDUE 3DR X 5
06AC6SOFTWAREGLU F:208 , PHE F:212 , SER F:222 , 3DR X:7BINDING SITE FOR RESIDUE 3DR X 6
07AC7SOFTWAREPHE F:212 , ARG J:15 , TYR J:18 , 3DR X:1 , 3DR X:6BINDING SITE FOR RESIDUE 3DR X 7
08AC8SOFTWARETHR F:241 , ASP F:242 , PHE F:243 , 3DR X:9 , 3DR X:10BINDING SITE FOR RESIDUE 3DR X 8
09AC9SOFTWAREASP F:242 , PHE F:243 , TRP F:244 , 3DR X:8 , 3DR X:10BINDING SITE FOR RESIDUE 3DR X 9
10BC1SOFTWAREHIS F:240 , THR F:241 , ASP F:242 , 3DR X:8 , 3DR X:9BINDING SITE FOR RESIDUE 3DR X 10

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M06)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M06)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M06)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M06)

(-) Exons   (0, 0)

(no "Exon" information available for 1M06)

(-) 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 d1m06f_ F: Microvirus capsid proteins                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1m06F00 F:10-431 Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1                                                                                                                                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Phage_F-1m06F01 F:187-429                                                                                                                                                                                                                          -- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Phage_F-1m06F02 F:187-429                                                                                                                                                                                                                          -- Pfam domains (2)
         Sec.struct. author .eeee..eeeeeee...eeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeehhhhhhhhhhhhhhhhhhh....eee.......hhhhh.......eeehhhhhhhhhhhhhhh...........hhhhhhhhhhhhhee.............................hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh............eeeeeeeeee.eeeee.........eeeeeeeeeeeeeeeee....eeeeeeeeee.........hhhhhh...hhhhhh.hhhhhh....eeee............eeee..hhhhh......hhhhhhh................hhhhhhh.hhhhhhhhh.......eeeeeeeeeeeee...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m06 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 d1m06g_ G: Microvirus capsid proteins                                                                                                                                                       SCOP domains
               CATH domains 1m06G00 G:1-187  [code=2.60.120.20, no name defined]                                                                                                                                        CATH domains
               Pfam domains Phage_G-1m06G01 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
                 1m06 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:24
 aligned with J_BPAL3 | P69548 from UniProtKB/Swiss-Prot  Length:24

    Alignment length:24
                                    10        20    
              J_BPAL3     1 MKKARRSPSRRKGARLWYVGGSQF  24
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author .hhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                 1m06 J   1 MKKARRSPSRRKGARLWYVGGSQF  24
                                    10        20    


Chain J from PDB  Type:PROTEIN  Length:24
 aligned with J_BPPHK | P69549 from UniProtKB/Swiss-Prot  Length:24

    Alignment length:24
                                    10        20    
              J_BPPHK     1 MKKARRSPSRRKGARLWYVGGSQF  24
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author .hhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                 1m06 J   1 MKKARRSPSRRKGARLWYVGGSQF  24
                                    10        20    


Chain X from PDB  Type:OTHER  Length:10
                                          
                 1m06 X   1 xxxxxxxxxx  10
                            ||||||||10
                            1-3DR|||10-3DR
                             2-3DR||| 
                              3-3DR|| 
                               4-3DR| 
                                5-3DR 
                                 6-3DR
                                  7-3DR
                                   8-3DR
                                    9-3DR
   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  (8, 15)

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_BPPHK | P69549)
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: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_BPAL3 | P69548)
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: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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  1m06
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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: 1m0f 1rb8
        VGF_BPAL3 | P08767: 1m0f 1rb8

(-) Related Entries Specified in the PDB File

1cd3 PROCAPSID OF THE BACTERIOPHAGE PHIX174
1gff ATOMIC STRUCTURE OF THE DEGRADED PROCAPSID PARTICLE OF THE BACTERIOPHAGE G4.
1phx DNA PACKAGING INTERMEDIATES OF THE BACTERIOPHAGE PHIX174
2bpa ATOMIC STRUCTURE OF THE SINGLE-STRANDED BACTERIOPHAGE PHIX174