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(-) Description

Title :  PSEUDO-ATOMIC MODEL OF A FIBERLESS ISOMETRIC VARIANT OF BACTERIOPHAGE PHI29
 
Authors :  M. C. Morais, K. H. Choi, J. S. Koti, P. R. Chipman, D. L. Anderson, M. G. Rossmann
Date :  22 Feb 05  (Deposition) - 26 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  7.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Phi29, Capsid, Icosahedral Virus Capsid, Hk97 Fold, Phage, Bacterial Immuno-Globulin, Big2, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Morais, K. H. Choi, J. S. Koti, P. R. Chipman, D. L. Anderson, M. G. Rossmann
Conservation Of The Capsid Structure In Tailed Dsdna Bacteriophages: The Pseudoatomic Structure Of Phi29
Mol. Cell V. 18 149 2005
PubMed-ID: 15837419  |  Reference-DOI: 10.1016/J.MOLCEL.2005.03.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAJOR HEAD PROTEIN
    Cell Line: PHI29
    Chains: A, B, C
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Taxid: 1423
    Gene: 8
    Organism Scientific: BACILLUS PHAGE PHI29
    Organism Taxid: 10756
    Synonym: LATE PROTEIN GP8

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1080)

Asymmetric Unit (1, 1080)
No.NameCountTypeFull Name
1UNK1080Mod. Amino Acid
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 1YXN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YXN)

(-) 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:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               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
                 1yxn A 104 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 836
                            |||||||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|||||||383|||||||766|||||||776|||||||786|||||||796|||||||806|||||||816|||||||826|||||||836
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Chain B from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               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
                 1yxn B 104 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 836
                            |||||||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|||||||383|||||||766|||||||776|||||||786|||||||796|||||||806|||||||816|||||||826|||||||836
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Chain C from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               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
                 1yxn C 104 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 836
                            |||||||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|||||||383|||||||766|||||||776|||||||786|||||||796|||||||806|||||||816|||||||826|||||||836
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   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 1YXN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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1f00 THE ATOMIC COORDINATES OF OF INTIMIN. RESIDUES 757-831, WHICH COMPRISE THE BIG2 DOMAIN OF INTIMIN, WERE FITTED INTO THE PHI29 CRYO-EM DENSITY AND CONSTITUTE ONE DOMAIN OF THE PSEUDO-ATOMIC MODEL OF THE PHI29 CAPSID PROTEIN GP8. RELATED ID: EMD-1116 RELATED DB: EMDB RELATED ID: EMD-1120 RELATED DB: EMDB
1ohg THE ATOMIC COORDINATES OF THE CAPSID PROTEIN OF HK97, WHICH WERE FITTED INTO THE PHI29 CRYO-EM DENSITY AND CONSTITUTE ONE DOMAIN OF THE PSEUDO-ATOMIC MODEL OF THE PHI29 CAPSID PROTEIN GP8.