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(-) Description

Title :  MODEL OF THE BACTERIOPHAGE T4 FIBRITIN BASED ON THE CRYO-EM RECONSTRUCTION OF THE CONTRACTED T4 TAIL CONTAINING THE PHAGE COLLAR AND WHISKERS
 
Authors :  A. Fokine, Z. Zhang, S. Kanamaru, V. D. Bowman, A. A. Aksyuk, F. Arisaka, M. G. Rossmann
Date :  12 Nov 12  (Deposition) - 06 Mar 13  (Release) - 15 May 13  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  25.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Bacteriophage T4, Phage Neck, Collar Whiskers, Fibritin, Gpwac, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Fokine, Z. Zhang, S. Kanamaru, V. D. Bowman, A. A. Aksyuk, F. Arisaka V. B. Rao, M. G. Rossmann
The Molecular Architecture Of The Bacteriophage T4 Neck.
J. Mol. Biol. V. 425 1731 2013
PubMed-ID: 23434847  |  Reference-DOI: 10.1016/J.JMB.2013.02.012

(-) Compounds

Molecule 1 - FIBRITIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: WAC
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: COLLAR PROTEIN, WHISKER ANTIGEN CONTROL PROTEIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3J2O)

(-) Sites  (0, 0)

(no "Site" information available for 3J2O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3J2O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3J2O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J2O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J2O)

(-) Exons   (0, 0)

(no "Exon" information available for 3J2O)

(-) 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 A from PDB  Type:PROTEIN  Length:362
 aligned with WAC_BPT4 | P10104 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:482
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482  
             WAC_BPT4     3 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQGILDVSGDIEALAQIGINKKDISDLKTLTSEHTEILNGTNNTVDSILADIGPFNAEANSVYRTIRNDLLWIKRELGQYTGQDINGLPVVGNPSSGMKHRIINNTDVITSQGIRLSELETKFIESDVGSLTIEVGNLREELGPKPPSFSQNVYSRLNEIDTKQTTVESDISAIKTSIGYPGNNSIITSVNTNTDNIASINLELNQSGGIKQRLTVIETSIGSDDIPSSIKGQIKDNTTSIESLNGIVGENTSSGLRANVSWLNQIVGTDSSGGQPSPPGSLLNRVSTIETSVSGLNNAVQNLQVEIGNNSAGIKGQVVALNTLVNGTNPNGSTVEERGLTNSIKANETNIASVTQEVNTAKGNISSLQGDVQALQEAGYIPEAPRDGQAYVRKDGEWVFLSTFL 484
               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
                 3j2o A   2 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQ----------------INKKDISDLKTLTSEHTEILNGTNNTVDSILADI-------------IRNDLLWIKREL--------------------MKHRIINNTDVITSQGIRL-------------SLTIEVGNLREEL----------VYSRLNEIDTKQTTVESDISAIKTSI------SIITSVNTNTDNIASINLE------IKQRLTVIETSI--------IKGQIKDNTTSI--------------LRANVSWLNQI--------------SLLNRVSTIETSVSGLNNAVQNLQVEIGNNSAGIKGQVVALNTLVNGTNPNGSTVEERGLTNSIKANETNIASVTQEVNTAKGNISSLQGDVQALQEAGYIPEAPRDGQAYVRKDGEWVFLSTFL 483
                                    11        21        31        41        51        61        71        |-         -     | 101       111       121        |-         -  |    151   |     -         -    |  181       191  |      -      |211        |-       231       241       251    |    - |     271       281      |291       | -      |311       | -         -  |    341  |      -       361       371       381       391       401       411       421       431       441       451       461       471       481  
                                                                                                         80               97                              130           144        155                  176               194           208         220        231                      256    263               281    288        299      308        319            334       344            359                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:362
 aligned with WAC_BPT4 | P10104 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:482
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482  
             WAC_BPT4     3 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQGILDVSGDIEALAQIGINKKDISDLKTLTSEHTEILNGTNNTVDSILADIGPFNAEANSVYRTIRNDLLWIKRELGQYTGQDINGLPVVGNPSSGMKHRIINNTDVITSQGIRLSELETKFIESDVGSLTIEVGNLREELGPKPPSFSQNVYSRLNEIDTKQTTVESDISAIKTSIGYPGNNSIITSVNTNTDNIASINLELNQSGGIKQRLTVIETSIGSDDIPSSIKGQIKDNTTSIESLNGIVGENTSSGLRANVSWLNQIVGTDSSGGQPSPPGSLLNRVSTIETSVSGLNNAVQNLQVEIGNNSAGIKGQVVALNTLVNGTNPNGSTVEERGLTNSIKANETNIASVTQEVNTAKGNISSLQGDVQALQEAGYIPEAPRDGQAYVRKDGEWVFLSTFL 484
               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
                 3j2o B   2 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQ----------------INKKDISDLKTLTSEHTEILNGTNNTVDSILADI-------------IRNDLLWIKREL--------------------MKHRIINNTDVITSQGIRL-------------SLTIEVGNLREEL----------VYSRLNEIDTKQTTVESDISAIKTSI------SIITSVNTNTDNIASINLE------IKQRLTVIETSI--------IKGQIKDNTTSI--------------LRANVSWLNQI--------------SLLNRVSTIETSVSGLNNAVQNLQVEIGNNSAGIKGQVVALNTLVNGTNPNGSTVEERGLTNSIKANETNIASVTQEVNTAKGNISSLQGDVQALQEAGYIPEAPRDGQAYVRKDGEWVFLSTFL 483
                                    11        21        31        41        51        61        71        |-         -     | 101       111       121        |-         -  |    151   |     -         -    |  181       191  |      -      |211        |-       231       241       251    |    - |     271       281      |291       | -      |311       | -         -  |    341  |      -       361       371       381       391       401       411       421       431       441       451       461       471       481  
                                                                                                         80               97                              130           144        155                  176               194           208         220        231                      256    263               281    288        299      308        319            334       344            359                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:362
 aligned with WAC_BPT4 | P10104 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:482
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482  
             WAC_BPT4     3 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQGILDVSGDIEALAQIGINKKDISDLKTLTSEHTEILNGTNNTVDSILADIGPFNAEANSVYRTIRNDLLWIKRELGQYTGQDINGLPVVGNPSSGMKHRIINNTDVITSQGIRLSELETKFIESDVGSLTIEVGNLREELGPKPPSFSQNVYSRLNEIDTKQTTVESDISAIKTSIGYPGNNSIITSVNTNTDNIASINLELNQSGGIKQRLTVIETSIGSDDIPSSIKGQIKDNTTSIESLNGIVGENTSSGLRANVSWLNQIVGTDSSGGQPSPPGSLLNRVSTIETSVSGLNNAVQNLQVEIGNNSAGIKGQVVALNTLVNGTNPNGSTVEERGLTNSIKANETNIASVTQEVNTAKGNISSLQGDVQALQEAGYIPEAPRDGQAYVRKDGEWVFLSTFL 484
               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
                 3j2o C   2 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQ----------------INKKDISDLKTLTSEHTEILNGTNNTVDSILADI-------------IRNDLLWIKREL--------------------MKHRIINNTDVITSQGIRL-------------SLTIEVGNLREEL----------VYSRLNEIDTKQTTVESDISAIKTSI------SIITSVNTNTDNIASINLE------IKQRLTVIETSI--------IKGQIKDNTTSI--------------LRANVSWLNQI--------------SLLNRVSTIETSVSGLNNAVQNLQVEIGNNSAGIKGQVVALNTLVNGTNPNGSTVEERGLTNSIKANETNIASVTQEVNTAKGNISSLQGDVQALQEAGYIPEAPRDGQAYVRKDGEWVFLSTFL 483
                                    11        21        31        41        51        61        71        |-         -     | 101       111       121        |-         -  |    151   |     -         -    |  181       191  |      -      |211        |-       231       241       251    |    - |     271       281      |291       | -      |311       | -         -  |    341  |      -       361       371       381       391       401       411       421       431       441       451       461       471       481  
                                                                                                         80               97                              130           144        155                  176               194           208         220        231                      256    263               281    288        299      308        319            334       344            359                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:144
 aligned with WAC_BPT4 | P10104 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   
             WAC_BPT4     3 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQGILDVSGDIEALAQIGINKKDISDLKTLTSEHTEILNGTNNTVDSILADIGPFNAEANSVYRTIRNDLLWIKRELGQYTGQDINGLPVVGNPSSGMKHRIINNTDVITSQGIRL 195
               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
                 3j2o D   2 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQ----------------INKKDISDLKTLTSEHTEILNGTNNTVDSILADI-------------IRNDLLWIKREL--------------------MKHRIINNTDVITSQGIRL 194
                                    11        21        31        41        51        61        71        |-         -     | 101       111       121        |-         -  |    151   |     -         -    |  181       191   
                                                                                                         80               97                              130           144        155                  176                  


Chain E from PDB  Type:PROTEIN  Length:144
 aligned with WAC_BPT4 | P10104 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   
             WAC_BPT4     3 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQGILDVSGDIEALAQIGINKKDISDLKTLTSEHTEILNGTNNTVDSILADIGPFNAEANSVYRTIRNDLLWIKRELGQYTGQDINGLPVVGNPSSGMKHRIINNTDVITSQGIRL 195
               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
                 3j2o E   2 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQ----------------INKKDISDLKTLTSEHTEILNGTNNTVDSILADI-------------IRNDLLWIKREL--------------------MKHRIINNTDVITSQGIRL 194
                                    11        21        31        41        51        61        71        |-         -     | 101       111       121        |-         -  |    151   |     -         -    |  181       191   
                                                                                                         80               97                              130           144        155                  176                  


Chain F from PDB  Type:PROTEIN  Length:144
 aligned with WAC_BPT4 | P10104 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   
             WAC_BPT4     3 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQGILDVSGDIEALAQIGINKKDISDLKTLTSEHTEILNGTNNTVDSILADIGPFNAEANSVYRTIRNDLLWIKRELGQYTGQDINGLPVVGNPSSGMKHRIINNTDVITSQGIRL 195
               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
                 3j2o F   2 DIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQ----------------INKKDISDLKTLTSEHTEILNGTNNTVDSILADI-------------IRNDLLWIKREL--------------------MKHRIINNTDVITSQGIRL 194
                                    11        21        31        41        51        61        71        |-         -     | 101       111       121        |-         -  |    151   |     -         -    |  181       191   
                                                                                                         80               97                              130           144        155                  176
   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 3J2O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J2O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J2O)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (WAC_BPT4 | P10104)
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  3j2o
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 Related Entries

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

UniProtKB/Swiss-Prot
        WAC_BPT4 | P10104: 1aa0 1avy 1ox3 1rfo 1v1h 1v1i 2bsg 2ibl 2kbl 3a1m 4mmq 4mmr 4mms 4mmt 4mmu 4mmv 4ncu 4ncv 4ncw

(-) Related Entries Specified in the PDB File

1aa0 CRYSTAL STRUCTURE OF THE C-TERMINAL REGION OF FIBRITIN
1ox3 CRYSTAL STRUCTURE OF MINI-FIBRITIN INCLUDING THE N-TERMINAL DOMAIN OF THE FIBRITIN MOLECULE.
2bsg A PREVIOUSLY PROPOSED MODEL OF FIBRITIN
3j2m
3j2n