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(-) Description

Title :  FITTING OF GP27 INTO CRYOEM RECONSTRUCTION OF BACTERIOPHAGE T4 BASEPLATE
 
Authors :  V. A. Kostyuchenko, P. G. Leiman, P. R. Chipman, S. Kanamaru, M. J. Van Raaij, F. Arisaka, V. V. Mesyanzhinov, M. G. Rossmann
Date :  19 May 03  (Deposition) - 09 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  12.00
Chains :  Asym./Biol. Unit :  D,E,F
Keywords :  Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. A. Kostyuchenko, P. G. Leiman, P. R. Chipman, S. Kanamaru, M. J. Van Raaij, F. Arisaka, V. V. Mesyanzhinov, M. G. Rossmann
Three-Dimensional Structure Of The Bacteriophage T4 Baseplate
Nat. Struct. Biol. V. 10 688 2003
PubMed-ID: 12923574  |  Reference-DOI: 10.1038/NSB970
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BASEPLATE STRUCTURAL PROTEIN GP27
    Chains: D, E, F
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: HUB PROTEIN 27

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : DEF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1PDJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PDJ)

(-) Sequences/Alignments

Asymmetric/Biological 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 D from PDB  Type:PROTEIN  Length:364
 aligned with BP27_BPT4 | P17172 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:373
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   
            BP27_BPT4     4 LQRPGYPNLSVKLFDSYDAWSNNRFVELAATITTLTMRDSLYGRNEGMLQFYDSKNIHTKMDGNEIIQISVANANDINNVKTRIYGCKHFSVSVDSKGDNIIAIELGTIHSIENLKFGRPFFPDAGESIKEMLGVIYQDRTLLTPAINAINAYVPDIPWTSTFENYLSYVREVALAVGSDKFVFVWQDIMGVNMMDYDMMINQEPYPMIVGEPSLIGQFIQELKYPLAYDFVWLTKSNPHKRDPMKNATIYAHSFLDSSIPMITTGKGENSIVVSRSGAYSEMTYRNGYEEAIRLQTMAQYDGYAKCSTIGNFNLTPGVKIIFNDSKNQFKTEFYVDEVIHELSNNNSVTHLYMFTNATKLETIDPVKVKNEF 376
               SCOP domains d1pdjd_ D: Bacteriophage T4 3D cryo-EM reconstruction                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................................................................................................................................................................................................---------...................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pdj D   4 LQRPGYPNLSVKLFDSYDAWSNNRFVELAATITTLTMRDSLYGRNEGMLQFYDSKNIHTKMDGNEIIQISVANANDINNVKTRIYGCKHFSVSVDSKGDNIIAIELGTIHSIENLKFGRPFFPDAGESIKEMLGVIYQDRTLLTPAINAINAYVPDIPWTSTFENYLSYVREVALAVGSDKFVFVWQDIMGVNMMDYDMMINQEPYPMIVGEPS---------KYPLAYDFVWLTKSNPHKRDPMKNATIYAHSFLDSSIPMITTGKGENSIVVSRSGAYSEMTYRNGYEEAIRLQTMAQYDGYAKCSTIGNFNLTPGVKIIFNDSKNQFKTEFYVDEVIHELSNNNSVTHLYMFTNATKLETIDPVKVKNEF 376
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   |     -   |   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   
                                                                                                                                                                                                                                               217       227                                                                                                                                                     


Chain E from PDB  Type:PROTEIN  Length:364
 aligned with BP27_BPT4 | P17172 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:373
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   
            BP27_BPT4     4 LQRPGYPNLSVKLFDSYDAWSNNRFVELAATITTLTMRDSLYGRNEGMLQFYDSKNIHTKMDGNEIIQISVANANDINNVKTRIYGCKHFSVSVDSKGDNIIAIELGTIHSIENLKFGRPFFPDAGESIKEMLGVIYQDRTLLTPAINAINAYVPDIPWTSTFENYLSYVREVALAVGSDKFVFVWQDIMGVNMMDYDMMINQEPYPMIVGEPSLIGQFIQELKYPLAYDFVWLTKSNPHKRDPMKNATIYAHSFLDSSIPMITTGKGENSIVVSRSGAYSEMTYRNGYEEAIRLQTMAQYDGYAKCSTIGNFNLTPGVKIIFNDSKNQFKTEFYVDEVIHELSNNNSVTHLYMFTNATKLETIDPVKVKNEF 376
               SCOP domains d1pdje_ E: Bacteriophage T4 3D cryo-EM reconstruction                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................................................................................................................................................................................................---------...................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pdj E   4 LQRPGYPNLSVKLFDSYDAWSNNRFVELAATITTLTMRDSLYGRNEGMLQFYDSKNIHTKMDGNEIIQISVANANDINNVKTRIYGCKHFSVSVDSKGDNIIAIELGTIHSIENLKFGRPFFPDAGESIKEMLGVIYQDRTLLTPAINAINAYVPDIPWTSTFENYLSYVREVALAVGSDKFVFVWQDIMGVNMMDYDMMINQEPYPMIVGEPS---------KYPLAYDFVWLTKSNPHKRDPMKNATIYAHSFLDSSIPMITTGKGENSIVVSRSGAYSEMTYRNGYEEAIRLQTMAQYDGYAKCSTIGNFNLTPGVKIIFNDSKNQFKTEFYVDEVIHELSNNNSVTHLYMFTNATKLETIDPVKVKNEF 376
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   |     -   |   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   
                                                                                                                                                                                                                                               217       227                                                                                                                                                     


Chain F from PDB  Type:PROTEIN  Length:364
 aligned with BP27_BPT4 | P17172 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:373
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   
            BP27_BPT4     4 LQRPGYPNLSVKLFDSYDAWSNNRFVELAATITTLTMRDSLYGRNEGMLQFYDSKNIHTKMDGNEIIQISVANANDINNVKTRIYGCKHFSVSVDSKGDNIIAIELGTIHSIENLKFGRPFFPDAGESIKEMLGVIYQDRTLLTPAINAINAYVPDIPWTSTFENYLSYVREVALAVGSDKFVFVWQDIMGVNMMDYDMMINQEPYPMIVGEPSLIGQFIQELKYPLAYDFVWLTKSNPHKRDPMKNATIYAHSFLDSSIPMITTGKGENSIVVSRSGAYSEMTYRNGYEEAIRLQTMAQYDGYAKCSTIGNFNLTPGVKIIFNDSKNQFKTEFYVDEVIHELSNNNSVTHLYMFTNATKLETIDPVKVKNEF 376
               SCOP domains d1pdjf_ F: Bacteriophage T4 3D cryo-EM reconstruction                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................................................................................................................................................................................................---------...................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pdj F   4 LQRPGYPNLSVKLFDSYDAWSNNRFVELAATITTLTMRDSLYGRNEGMLQFYDSKNIHTKMDGNEIIQISVANANDINNVKTRIYGCKHFSVSVDSKGDNIIAIELGTIHSIENLKFGRPFFPDAGESIKEMLGVIYQDRTLLTPAINAINAYVPDIPWTSTFENYLSYVREVALAVGSDKFVFVWQDIMGVNMMDYDMMINQEPYPMIVGEPS---------KYPLAYDFVWLTKSNPHKRDPMKNATIYAHSFLDSSIPMITTGKGENSIVVSRSGAYSEMTYRNGYEEAIRLQTMAQYDGYAKCSTIGNFNLTPGVKIIFNDSKNQFKTEFYVDEVIHELSNNNSVTHLYMFTNATKLETIDPVKVKNEF 376
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   |     -   |   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   
                                                                                                                                                                                                                                               217       227
   Legend:   → Mismatch (orange background)
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  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, 3)

Asymmetric/Biological Unit
(-)
Class: Low resolution protein structures (283)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1PDJ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain D,E,F   (BP27_BPT4 | P17172)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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: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
        BP27_BPT4 | P17172: 1k28 1wth 2z6b 5iv5

(-) Related Entries Specified in the PDB File

1k28 GP27 IS A PART OF THE CELL-PUNCTURING DEVICE, PART OF THE BASEPLATE RELATED ID: EMD-1048 RELATED DB: EMDB