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(-) Description

Title :  STRUCTURE OF THE RECEPTOR-BINDING DOMAIN OF THE BACTERIOPHAGE T4 SHORT TAIL FIBRE
 
Authors :  E. Thomassen, G. Gielen, M. Schuetz, S. Miller, M. J. Van Raaij
Date :  11 Feb 03  (Deposition) - 24 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Structural Protein, Fibrous Protein, Lipo-Polysaccharide Binding, Bacteriophage Structural Protein, Baseplate Protein, Gene Product 12 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Thomassen, G. Gielen, M. Schuetz, G. Schoehn, J. P. Abrahams, S. Miller, M. J. Van Raaij
The Structure Of The Receptor-Binding Domain Of The Bacteriophage T4 Short Tail Fibre Reveals A Knitted Trimeric Metal-Binding Fold
J. Mol. Biol. V. 331 361 2003
PubMed-ID: 12888344  |  Reference-DOI: 10.1016/S0022-2836(03)00755-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIOPHAGE T4 SHORT TAIL FIBRE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21+
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Variant: DE3
    Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 330-527
    Organism Scientific: BACTERIOPHAGE T4
    Organism Taxid: 10665
    Other Details: VARIANT AS PRESENT IN LABORATORY OF S. MILLER. CO-EXPRESSION WITH GP57 CHAPERONE
    Strain: D

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2SO42Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1CIT3Ligand/IonCITRIC ACID
2SO46Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:464 , ARG A:465 , ARG A:480 , GLN A:495 , TYR A:500 , CIT A:1528 , HOH A:2470 , HOH A:2512 , HOH A:2513BINDING SITE FOR RESIDUE SO4 A1529
2AC2SOFTWARESER A:386 , SER A:387 , HOH A:2514 , HOH A:2515 , HOH A:2516BINDING SITE FOR RESIDUE SO4 A1530
3AC3SOFTWAREHIS A:445 , HIS A:447BINDING SITE FOR RESIDUE ZN A1531
4AC4SOFTWAREGLY A:421 , TYR A:454 , ASP A:455 , ASP A:456 , ARG A:465 , ARG A:480 , PRO A:492 , ASN A:497 , SER A:498 , SO4 A:1529 , HOH A:2510 , HOH A:2511 , HOH A:2512BINDING SITE FOR RESIDUE CIT A1528

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OCY)

(-) 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:198
 aligned with FIB12_BPT4 | P10930 from UniProtKB/Swiss-Prot  Length:527

    Alignment length:198
                                   339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519        
           FIB12_BPT4   330 RIVTQNEIDRTIPVGAIMMWAADSLPSDAWRFCHGGTVSASDCPLYASRIGTRYGGNPSNPGLPDMRGLFVRGSGRGSHLTNPNVNGNDQFGKPRLGVGCTGGYVGEVQIQQMSYHKHAGGFGEHDDLGAFGNTRRSNFVGTRKGLDWDNRSYFTNDGYEIDPESQRNSKYTLNRPELIGNETRPWNISLNYIIKVKE 527
               SCOP domains d1ocya_ A: Receptor-binding domain of short tail fibre protein gp12                                                                                                                                    SCOP domains
               CATH domains 1ocyA01 A:330-396,A:519-527                                        1ocyA02 A:397-518 receptor-binding domain of the bacteriophage t4 short tail fibre, domain 2                              1ocyA01   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhh....eeee.........eee..........hhhhhhhh..........................hhhhhhhhhh............................................................................hhhhhhhhhh..................eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ocy A 330 RVVTQNEIDRTIPVGAIMMWAADSLPSDAWRFCHGGTVSASDCPLYASRIGTRYGGSSSNPGLPDMRGLFVRGSGRGSHLTNPNVNGNDQFGKPRLGVGCTGGYVGEVQKQQMSYHKHAGGFGEYDDSGAFGNTRRSNFVGTRKGLDWDNRSYFTNDGYEIDPASQRNSRYTLNRPELIGNETRPWNISLNYIIKVKE 527
                                   339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519        


Chain A from PDB  Type:PROTEIN  Length:198
 aligned with Q38160_BPT2 | Q38160 from UniProtKB/TrEMBL  Length:527

    Alignment length:198
                                   339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519        
          Q38160_BPT2   330 RVVTQNEIDRTIPVGAIMMWAADSLPSDAWRFCHGGTVSASDCPLYASRIGTRYGGTSSNPGLPDMRGLFVRGSGRGSHLTNPNVNGNDQFGKPRLGVGCTGGYVGEVQKQQMSYHKHAGGFGEYDDSGAFGNTRRSNFVGTRKGLDWDNRSYFTNDGYEIDPASQRNSRYTLNRPELIGNETRPWNISLNYIIKVKE 527
               SCOP domains d1ocya_ A: Receptor-binding domain of short tail fibre protein gp12                                                                                                                                    SCOP domains
               CATH domains 1ocyA01 A:330-396,A:519-527                                        1ocyA02 A:397-518 receptor-binding domain of the bacteriophage t4 short tail fibre, domain 2                              1ocyA01   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhh....eeee.........eee..........hhhhhhhh..........................hhhhhhhhhh............................................................................hhhhhhhhhh..................eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ocy A 330 RVVTQNEIDRTIPVGAIMMWAADSLPSDAWRFCHGGTVSASDCPLYASRIGTRYGGSSSNPGLPDMRGLFVRGSGRGSHLTNPNVNGNDQFGKPRLGVGCTGGYVGEVQKQQMSYHKHAGGFGEYDDSGAFGNTRRSNFVGTRKGLDWDNRSYFTNDGYEIDPASQRNSRYTLNRPELIGNETRPWNISLNYIIKVKE 527
                                   339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (FIB12_BPT4 | P10930)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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:0019012    virion    The complete fully infectious extracellular virus particle.

Chain A   (Q38160_BPT2 | Q38160)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FIB12_BPT4 | P10930: 1h6w 1pdi 5iv5

(-) Related Entries Specified in the PDB File

1h6w CRYSTAL STRUCTURE OF A HEAT- AND PROTEASE- STABLE FRAGMENT OF THE BACTERIOPHAGE T4 SHORT FIBRE