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(-) Description

Title :  CRYSTAL STRUCTURE OF VACCINIA VIRUS L1 PROTEIN
 
Authors :  H. P. Su, S. C. Garman, T. J. Allison, C. Fogg, B. Moss, D. N. Garboczi
Date :  31 Jan 05  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Vaccinia Virus, Orthopox, Variola Virus, Smallpox, L1, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. Su, S. C. Garman, T. J. Allison, C. Fogg, B. Moss, D. N. Garboczi
The 1. 51-Angstrom Structure Of The Poxvirus L1 Protein, A Target Of Potent Neutralizing Antibodies.
Proc. Natl. Acad. Sci. Usa V. 102 4240 2005
PubMed-ID: 15761054  |  Reference-DOI: 10.1073/PNAS.0501103102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VIRION MEMBRANE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLM
    Expression System Strain: BL21(DE3)-CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: L1
    Organism Scientific: VACCINIA VIRUS
    Organism Taxid: 10245

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1YPY)

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:34 -A:57
2A:49 -A:136
3A:116 -A:158
4B:34 -B:57
5B:49 -B:136
6B:116 -B:158

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 1YPY)

(-) 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:182
 aligned with L1_VACCW | P07612 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:182
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183  
             L1_VACCW     4 AASIQTTVNTLSERISSKLEQEANASAQTKCDIEIGNFYIRQNHGCNLTVKNMCSADADAQLDAVLSAATETYSGLTPEQKAYVPAMFTAALNIQTSVNTVVRDFENYVKQTCNSSAVVDNKLKIQNVIIDECYGAPGSPTNLEFINTGSSKGNCAIKALMQLTTKATTQIAPKQVAGTGVQ 185
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeeeeee.eeeeeee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhh....eeeeeeeeee......eeeeeee..hhhhhhhhhhhhhhhhhhhhhhh..ee..ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ypy A   4 AASIQTTVNTLSERISSKLEQEANASAQTKCDIEIGNFYIRQNHGCNLTVKNMCSADADAQLDAVLSAATETYSGLTPEQKAYVPAMFTAALNIQTSVNTVVRDFENYVKQTCNSSAVVDNKLKIQNVIIDECYGAPGSPTNLEFINTGSSKGNCAIKALMQLTTKATTQIAPKQVAGTGVQ 185
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183  


Chain B from PDB  Type:PROTEIN  Length:168
 aligned with L1_VACCW | P07612 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:168
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164        
             L1_VACCW     5 ASIQTTVNTLSERISSKLEQEANASAQTKCDIEIGNFYIRQNHGCNLTVKNMCSADADAQLDAVLSAATETYSGLTPEQKAYVPAMFTAALNIQTSVNTVVRDFENYVKQTCNSSAVVDNKLKIQNVIIDECYGAPGSPTNLEFINTGSSKGNCAIKALMQLTTKATT 172
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeee.eeeeeee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee......eeeeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ypy B   5 ASIQTTVNTLSERISSKLEQEANASAQTKCDIEIGNFYIRQNHGCNLTVKNMCSADADAQLDAVLSAATETYSGLTPEQKAYVPAMFTAALNIQTSVNTVVRDFENYVKQTCNSSAVVDNKLKIQNVIIDECYGAPGSPTNLEFINTGSSKGNCAIKALMQLTTKATT 172
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164
   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  (0, 0)

(no "SCOP Domain" information available for 1YPY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (L1_VACCW | P07612)
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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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        L1_VACCW | P07612: 2i9l 4u6h

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