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(-) Description

Title :  THE ATOMIC STRUCTURE OF THE DEGRADED PROCAPSID PARTICLE OF THE BACTERIOPHAGE G4: INDUCED STRUCTURAL CHANGES IN THE PRESENCE OF CALCIUM IONS AND FUNCTIONAL IMPLICATIONS
 
Authors :  M. G. Rossmann
Date :  06 Nov 95  (Deposition) - 03 Apr 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  1,2,3
Biol. Unit 1:  1,2,3  (60x)
Keywords :  Coat Protein, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Mckenna, B. R. Bowman, L. L. Ilag, M. G. Rossmann, B. A. Fane
Atomic Structure Of The Degraded Procapsid Particle Of The Bacteriophage G4: Induced Structural Changes In The Presence Of Calcium Ions And Functional Implications.
J. Mol. Biol. V. 256 736 1996
PubMed-ID: 8642594  |  Reference-DOI: 10.1006/JMBI.1996.0121
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
    Chains: 1
    Engineered: YES
    Expression System: ESCHERICHIA COLI C
    Expression System Strain: C
    Expression System Taxid: 498388
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE G4
    Organism Taxid: 10843
 
Molecule 2 - BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
    Chains: 2
    Engineered: YES
    Expression System: ESCHERICHIA COLI C
    Expression System Strain: C
    Expression System Taxid: 498388
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE G4
    Organism Taxid: 10843
 
Molecule 3 - BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
    Chains: 3
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE G4
    Organism Taxid: 10843

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : 123
Biological Unit 1 (60x): 123

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1GFF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GFF)

(-) 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 1 from PDB  Type:PROTEIN  Length:417
 aligned with VGF_BPG4 | P03642 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:417
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       
             VGF_BPG4    11 VPHDLSHLVFEAGKIGRLKTISWTPVVAGDSFECDMVGAIRLSPLRRGLAVDSRVDIFSFYIPHRHIYGQQWINFMKDGVNASPLPPVTCSSGWDSAAYLGTIPSSTLKVPKFLHQGYLNIYNNYFKPPWSDDLTYANPSNMPSEDYKWGVRVANLKSIWTAPLPPDTRTSENMTTGTSTIDIMGLQAAYAKLHTEQERDYFMTRYRDIMKEFGGHTSYDGDNRPLLLMRSEFWASGYDVDGTDQSSLGQFSGRVQQTFNHKVPRFYVPEHGVIMTLAVTRFPPTHEMEMHYLVGKENLTYTDIACDPALMANLPPREVSLKEFFHSSPDSAKFKIAEGQWYRTQPDRVAFPYNALDGFPFYSALPSTELKDRVLVNTNNYDEIFQSMQLAHWNMQTKFNINVYRHMPTTRDSIMTS 427
               SCOP domains d1gff1_ 1: Microvirus capsid proteins                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1gff100 1:10-426 Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee....eeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee......hhhhhhhhh.................................hhhhhhhhhhhhhh..................hhhhhh.................................hhhhhhhhhhhhhhhhhhh....hhhhhh..............eeeeeeeeeeeeeeeee........eeeeeeeeeeeeeeeee....eeeeeeeeee..........hhhhh....hhhh...hhhh..........................................................hhhhh..................eeeeeeeeeeeee....hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gff 1  10 VPHDLSHLVFEAGKIGRLKTISWTPVVAGDSFECDMVGAIRLSPLRRGLAVDSRVDIFSFYIPHRHIYGQQWINFMKDGVNASPLPPVTCSSGWDSAAYLGTIPSSTLKVPKFLHQGYLNIYNNYFKPPWSDDLTYANPSNMPSEDYKWGVRVANLKSIWTAPLPPDTRTSENMTTGTSTIDIMGLQAAYAKLHTEQERDYFMTRYRDIMKEFGGHTSYDGDNRPLLLMRSEFWASGYDVDGTDQSSLGQFSGRVQQTFNHKVPRFYVPEHGVIMTLAVTRFPPTHEMEMHYLVGKENLTYTDIACDPALMANLPPREVSLKEFFHSSPDSAKFKIAEGQWYRTQPDRVAFPYNALDGFPFYSALPSTDLKDRVLVNTNNYDEIFQSMQLAHWNMQTKFNINVYRHMPTTRDSIMTS 426
                                    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       


Chain 2 from PDB  Type:PROTEIN  Length:177
 aligned with G_BPG4 | P03644 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
               G_BPG4     1 MFQKFISKHNAPINSTQLAATKTPAVAAPVLSVPNLSRSTILINATTTAVTTHSGLCHVVRIDETNPTNHHALSIAGSLSNVPADMIAFAIRFEVADGVVPTAVPALYDVYPIETFNNGKAISFKDAVTIDSHPRTVGNDVYAGIMLWSNAWTASTISGVLSVNQVNREATVLQPLK 177
               SCOP domains d1gff2_ 2: Microvirus capsid proteins                                                                                                                                             SCOP domains
               CATH domains 1gff200 2:1-177  [code=2.60.120.20, no name defined]                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................................eeeeeeee.........eeeeeee........eeeeeeeeee.......eeeeeeeeee............eee...eeee...eeeeeeeeeee......eeeeeeeeee..........eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gff 2   1 MFQKFISKHNAPINSTQLAATKTPAVAAPVLSVPNLSRSTILINATTTAVTTHSGLCHVVRIDETNPTNHHALSIAGSLSNVPADMIAFAIRFEVADGVVPTAVPALYDVYPIETFNNGKAISFKDAVTIDSHPRTVGNDVYAGIMLWSNAWTASTISGVLSVNQVNREATVLQPLK 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       


Chain 3 from PDB  Type:PROTEIN  Length:12
 aligned with J_BPG4 | P03652 from UniProtKB/Swiss-Prot  Length:25

    Alignment length:12
                                    23  
               J_BPG4    14 GARLWYVGGTQY  25
               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
                 1gff 3  14 GARLWYVGGTQY  25
                                    23
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

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

(-) Gene Ontology  (8, 12)

Asymmetric Unit(hide GO term definitions)
Chain 1   (VGF_BPG4 | P03642)
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 2   (G_BPG4 | P03644)
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 3   (J_BPG4 | P03652)
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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