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(-) Description

Title :  HK97-LIKE FOLD FITTED INTO 3D RECONSTRUCTION OF BACTERIOPHAGE CW02
 
Authors :  P. S. Shen, M. J. Domek, E. Sanz-Garcia, A. Makaju, R. Taylor, M. Culumbe D. P. Breakwell, J. T. Prince, D. M. Belnap
Date :  31 Jan 12  (Deposition) - 30 May 12  (Release) - 25 Jul 12  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  16.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A,B,C,D,E,F,G  (60x)
Keywords :  Halophage, Bacteriophage Hk97, Bacteriophage T7, T7-Like Phage, Turret, Extremophile, Great Salt Lake, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Shen, M. J. Domek, E. Sanz-Garcia, A. Makaju, R. M. Taylor, R. Hoggan, M. D. Culumber, C. J. Oberg, D. P. Breakwell, J. T. Prince, D. M. Belnap
Sequence And Structural Characterization Of Great Salt Lake Bacteriophage Cw02, A Member Of The T7-Like Supergroup.
J. Virol. V. 86 7907 2012
PubMed-ID: 22593163  |  Reference-DOI: 10.1128/JVI.00407-12

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B, C, D, E, F, G
    Fragment: SEE REMARK 999
    Organism Scientific: GREAT SALT LAKE BACTERIOPHAGE CW02
    Organism Taxid: 32644
    Synonym: HK97 FOLD

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3J1A)

(-) Sites  (0, 0)

(no "Site" information available for 3J1A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3J1A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3J1A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J1A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J1A)

(-) Exons   (0, 0)

(no "Exon" information available for 3J1A)

(-) 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 A from PDB  Type:PROTEIN  Length:128
 aligned with CAPSD_BPHK7 | P49861 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:197
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       
          CAPSD_BPHK7   184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLNGDGTGDNLEGLNKVATAYDTSLNATGDTRADIIAHAIYQVTESEFSASGIVLNPRDWHNIALLKDNEGRYIFGGPQAFTSNIMWGLPVVPTKAQAAGTFTVGGFDMASQVWDRMDATVEVSREDRDNFVKNMLTILCEERLALAHYRPTAIIKGT 380
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh-----------------------------...............----eeeehhhhhhhhhh-------------------ee..eeeee-------eeeeehhhhheeeee.eeeeeeee----------eeeeeeeeee.eee.hhh.eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j1a A 184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLN-----------------------------ADIIAHAIYQVTESE----GIVLNPRDWHNIAL-------------------IMWGLPVVP-------TFTVGGFDMASQVWDRMDATVEVS----------MLTILCEERLALAHYRPTAIIKGT 380
                                   193       203       213       223 |       -         -         - |     263     |   -|      283   |     -         -   |   313 |     323       333       343  |      -   |   363       373       
                                                                   225                           255           269  274          287                 307     315     323                    346        357                       


Chain B from PDB  Type:PROTEIN  Length:128
 aligned with CAPSD_BPHK7 | P49861 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:197
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       
          CAPSD_BPHK7   184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLNGDGTGDNLEGLNKVATAYDTSLNATGDTRADIIAHAIYQVTESEFSASGIVLNPRDWHNIALLKDNEGRYIFGGPQAFTSNIMWGLPVVPTKAQAAGTFTVGGFDMASQVWDRMDATVEVSREDRDNFVKNMLTILCEERLALAHYRPTAIIKGT 380
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeeeehhhhhhh.........................-----------------------------...............----eeeehhhhhhhhhh-------------------ee..eeeee-------eeeeehhhhheeeee.eeeeeeee----------eeeeeeeeee.eee.hhh.eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j1a B 184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLN-----------------------------ADIIAHAIYQVTESE----GIVLNPRDWHNIAL-------------------IMWGLPVVP-------TFTVGGFDMASQVWDRMDATVEVS----------MLTILCEERLALAHYRPTAIIKGT 380
                                   193       203       213       223 |       -         -         - |     263     |   -|      283   |     -         -   |   313 |     323       333       343  |      -   |   363       373       
                                                                   225                           255           269  274          287                 307     315     323                    346        357                       


Chain C from PDB  Type:PROTEIN  Length:128
 aligned with CAPSD_BPHK7 | P49861 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:197
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       
          CAPSD_BPHK7   184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLNGDGTGDNLEGLNKVATAYDTSLNATGDTRADIIAHAIYQVTESEFSASGIVLNPRDWHNIALLKDNEGRYIFGGPQAFTSNIMWGLPVVPTKAQAAGTFTVGGFDMASQVWDRMDATVEVSREDRDNFVKNMLTILCEERLALAHYRPTAIIKGT 380
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................................-----------------------------...............----eeeehhhhhhhhhh-------------------ee..eeeee-------eeeeehhhhh..............----------eeeeeeeeeeeeee.hhh.eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j1a C 184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLN-----------------------------ADIIAHAIYQVTESE----GIVLNPRDWHNIAL-------------------IMWGLPVVP-------TFTVGGFDMASQVWDRMDATVEVS----------MLTILCEERLALAHYRPTAIIKGT 380
                                   193       203       213       223 |       -         -         - |     263     |   -|      283   |     -         -   |   313 |     323       333       343  |      -   |   363       373       
                                                                   225                           255           269  274          287                 307     315     323                    346        357                       


Chain D from PDB  Type:PROTEIN  Length:128
 aligned with CAPSD_BPHK7 | P49861 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:197
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       
          CAPSD_BPHK7   184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLNGDGTGDNLEGLNKVATAYDTSLNATGDTRADIIAHAIYQVTESEFSASGIVLNPRDWHNIALLKDNEGRYIFGGPQAFTSNIMWGLPVVPTKAQAAGTFTVGGFDMASQVWDRMDATVEVSREDRDNFVKNMLTILCEERLALAHYRPTAIIKGT 380
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeeee................................-----------------------------...............----eeeehhhhhhhhhh-------------------ee..eeeee-------eeeee.hhh.eeeeeeeeeeeeee----------eeeeeeeeeeeeee.hhh.eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j1a D 184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLN-----------------------------ADIIAHAIYQVTESE----GIVLNPRDWHNIAL-------------------IMWGLPVVP-------TFTVGGFDMASQVWDRMDATVEVS----------MLTILCEERLALAHYRPTAIIKGT 380
                                   193       203       213       223 |       -         -         - |     263     |   -|      283   |     -         -   |   313 |     323       333       343  |      -   |   363       373       
                                                                   225                           255           269  274          287                 307     315     323                    346        357                       


Chain E from PDB  Type:PROTEIN  Length:128
 aligned with CAPSD_BPHK7 | P49861 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:197
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       
          CAPSD_BPHK7   184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLNGDGTGDNLEGLNKVATAYDTSLNATGDTRADIIAHAIYQVTESEFSASGIVLNPRDWHNIALLKDNEGRYIFGGPQAFTSNIMWGLPVVPTKAQAAGTFTVGGFDMASQVWDRMDATVEVSREDRDNFVKNMLTILCEERLALAHYRPTAIIKGT 380
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeeeehhhhhhh.........................-----------------------------...............----eeeehhhhhhhhhh-------------------ee..eeeee-------eeeee.hhh.eeeee.eeeeeeee----------eeeeeeeeee.eee.hhh.eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j1a E 184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLN-----------------------------ADIIAHAIYQVTESE----GIVLNPRDWHNIAL-------------------IMWGLPVVP-------TFTVGGFDMASQVWDRMDATVEVS----------MLTILCEERLALAHYRPTAIIKGT 380
                                   193       203       213       223 |       -         -         - |     263     |   -|      283   |     -         -   |   313 |     323       333       343  |      -   |   363       373       
                                                                   225                           255           269  274          287                 307     315     323                    346        357                       


Chain F from PDB  Type:PROTEIN  Length:128
 aligned with CAPSD_BPHK7 | P49861 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:197
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       
          CAPSD_BPHK7   184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLNGDGTGDNLEGLNKVATAYDTSLNATGDTRADIIAHAIYQVTESEFSASGIVLNPRDWHNIALLKDNEGRYIFGGPQAFTSNIMWGLPVVPTKAQAAGTFTVGGFDMASQVWDRMDATVEVSREDRDNFVKNMLTILCEERLALAHYRPTAIIKGT 380
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh.........................-----------------------------...............----eeeehhhhhhhhhh-------------------ee..eeeee-------eeeee.hhh...............----------eeeeeeeeeeeeee.hhh.eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j1a F 184 KTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLN-----------------------------ADIIAHAIYQVTESE----GIVLNPRDWHNIAL-------------------IMWGLPVVP-------TFTVGGFDMASQVWDRMDATVEVS----------MLTILCEERLALAHYRPTAIIKGT 380
                                   193       203       213       223 |       -         -         - |     263     |   -|      283   |     -         -   |   313 |     323       333       343  |      -   |   363       373       
                                                                   225                           255           269  274          287                 307     315     323                    346        357                       


Chain G from PDB  Type:PROTEIN  Length:130
 aligned with CAPSD_BPHK7 | P49861 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:199
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371         
          CAPSD_BPHK7   182 NVKTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLNGDGTGDNLEGLNKVATAYDTSLNATGDTRADIIAHAIYQVTESEFSASGIVLNPRDWHNIALLKDNEGRYIFGGPQAFTSNIMWGLPVVPTKAQAAGTFTVGGFDMASQVWDRMDATVEVSREDRDNFVKNMLTILCEERLALAHYRPTAIIKGT 380
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--------hhhhhhee------------...............----eeeehhhhhhhhhh-----------------------eeeee-------eeeeehhhhheeeeeeeeeeeeee----------eeeeeeeeeeeeee-----eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j1a G 182 NVKTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLNG--------GLNKVATA------------ADIIAHAIYQVTESE----GIVLNPRDWHNIAL-----------------------LPVVP-------TFTVGGFDMASQVWDRMDATVEVS----------MLTILCEERLALAH-----IIKGT 380
                                   191       201       211       221    |    -   |   241|        -   |   261       | -  |    281     |   -         -       311   |     - |     331       341    |    -     | 361        |-    |    
                                                                      226      235    242          255           269  274          287                     311 315     323                    346        357          370   376
   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  (0, 0)

(no "SCOP Domain" information available for 3J1A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J1A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J1A)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G   (CAPSD_BPHK7 | P49861)
biological process
    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:0039620    T=7 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=7 symmetry. The T=7 capsid is composed of 12 pentameric and 60 hexameric capsomeres.
    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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  3j1a
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_BPHK7 | P49861: 1if0 1ohg 2frp 2fs3 2fsy 2ft1 2fte 2gp1 3ddx 3e8k 3qpr

(-) Related Entries Specified in the PDB File

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