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(-) Description

Title :  MAJOR TROPISM DETERMINANT P3C VARIANT
 
Authors :  S. A. Mcmahon, J. L. Miller, J. A. Lawton, P. Ghosh
Date :  11 Feb 05  (Deposition) - 20 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  C-Type Lectin, Beta Sandwich, Beta Prism, Variability, Diversity- Generating Retroelement, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Mcmahon, J. L. Miller, J. A. Lawton, D. E. Kerkow, A. Hodes, M. A. Marti-Renom, S. Doulatov, E. Narayanan, A. Sali, J. F. Miller, P. Ghosh
The C-Type Lectin Fold As An Evolutionary Solution For Massive Sequence Variation
Nat. Struct. Mol. Biol. V. 12 886 2005
PubMed-ID: 16170324  |  Reference-DOI: 10.1038/NSMB992

(-) Compounds

Molecule 1 - MAJOR TROPISM DETERMINANT (MTD-P3C)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: BORDETELLA PHAGE BPP-1
    Organism Taxid: 194699

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MMC2Ligand/IonMETHYL MERCURY ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MMC6Ligand/IonMETHYL MERCURY ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:313 , HOH A:400BINDING SITE FOR RESIDUE MG A 383
2AC2SOFTWAREGLY A:249 , LYS A:250 , ARG A:251 , CYS A:375BINDING SITE FOR RESIDUE MMC A 384
3AC3SOFTWARETYR A:112 , VAL A:113 , CYS A:114 , THR A:118 , VAL A:119 , ARG A:120BINDING SITE FOR RESIDUE MMC A 382

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YU1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YU1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YU1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YU1)

(-) Exons   (0, 0)

(no "Exon" information available for 1YU1)

(-) 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:376
 aligned with FIBD_BPBPP | Q775D6 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:376
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374      
           FIBD_BPBPP     5 VQFRGGTTAQHATFTGAAREITVDTDKNTVVVHDGATAGGFPLARHDLVKTAFIKADKSAVAFTRTGNATASIKAGTIVEVNGKLVQFTADTAITMPALTAGTDYAIYVCDDGTVRADSNFSAPTGYTSTTARKVGGFHYAPGSNAAAQAGGNTTAQINEYSLWDIKFRPAALDPRGMTLVAGAFWADIYLLGVNHLTDGTSKYNVTIADGSASPKKSTKFGGDGSAAYSDGAWYNFAEVMTHHGKRLPNYNEFQALAFGTTEATSSGGTDVPTTGVNGTGATSAWNIFTSKWGVVQASGCLWTWGNEFGGVNGASEYTANTGGRGSVYAQPAAALFGGAWNGTSLSGSRAALWYSGPSFSFAFFGARGVCDHLIL 380
               SCOP domains d1yu1a1 A:5-170 Major tropism determinant (Mtd), N-terminal domain                                                                                                    d1yu1a2 A:171-380 Major tropism determinant (Mtd), C-terminal domain                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhhhh.......eeee....eeee........ee..hhhhhh..ee........eeeee..eeee...eeeee..eeeee...ee.........eeeeeeee....eeee.............eeeeeeeeee...............ee.hhhhee..eee.......eeee...eeee......hhhhhh................................hhhhhhhhhhhh.....hhhhhhhhh..........................hhhhhh............eeeeeeeeeee..................eeeeee.....hhhhh....ee...........ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yu1 A   5 VQFRGGTTAQHATFTGAAREITVDTDKNTVVVHDGATAGGFPLARHDLVKTAFIKADKSAVAFTRTGNATASIKAGTIVEVNGKLVQFTADTAITMPALTAGTDYAIYVCDDGTVRADSNFSAPTGYTSTTARKVGGFHYAPGSNAAAQAGGNTTAQINEYSLWDIKFRPAALDPRGMTLVAGAFWADIYLLGVNHLTDGTSKYNVTIADGSASPKKSTKFGGDGSAAYSDGAWYNFAEVMTHHGKRLPNYNEFQALAFGTTEATSSGGTDVPTTGVNGTGATSAWNIFTSKWGVVQASGCLWTWGNEFGGVNGASEYTANTGGRGSVYAQPAAALFGGNWSNTSHSGSRAALWYVGPSNSFAGIGARGVCDHLIL 380
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YU1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YU1)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (FIBD_BPBPP | Q775D6)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FIBD_BPBPP | Q775D6: 1yu0 1yu2 1yu3 1yu4 2iou

(-) Related Entries Specified in the PDB File

1yu01yu21yu3
1yu4