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(-) Description

Title :  CRYSTAL STRUCTURE OF VARIABLE LYMPHOCYTE RECEPTOR VLRA.R5.1
 
Authors :  L. Deng, C. A. Velikovsky, R. A. Mariuzza
Date :  04 Mar 10  (Deposition) - 30 Jun 10  (Release) - 11 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Variable Lymphocyte Receptor, Adaptive Immunity, Antibody, T Cell, B Cell, Leucine-Rich Repeat, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Deng, C. A. Velikovsky, G. Xu, L. M. Iyer, S. Tasumi, M. C. Kerzic, M. F. Flajnik, L. Aravind, Z. Pancer, R. A. Mariuzza
A Structural Basis For Antigen Recognition By The T Cell-Like Lymphocytes Of Sea Lamprey.
Proc. Natl. Acad. Sci. Usa V. 107 13408 2010
PubMed-ID: 20616002  |  Reference-DOI: 10.1073/PNAS.1005475107

(-) Compounds

Molecule 1 - VARIABLE LYMPHOCYTE RECEPTOR A DIVERSITY REGION
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 CODONPLUS(DE3)
    Expression System Taxid: 562
    Expression System Vector: PT7-7
    Expression System Vector Type: PLASMID
    Fragment: ECTODOMAIN
    Gene: VLRA
    Organism Common: MARINE LAMPREY
    Organism Scientific: PETROMYZON MARINUS
    Organism Taxid: 7757

 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 3M19)

(-) Sites  (0, 0)

(no "Site" information available for 3M19)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:3 -A:11
2A:9 -A:20
3A:192 -A:228
4A:195 -A:246
5B:3 -B:11
6B:9 -B:20
7B:192 -B:228
8B:195 -B:246

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M19)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M19)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M19)

(-) Exons   (0, 0)

(no "Exon" information available for 3M19)

(-) 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:237
 aligned with C7B6Z3_PETMA | C7B6Z3 from UniProtKB/TrEMBL  Length:250

    Alignment length:244
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    
         C7B6Z3_PETMA     3 CETVTGCTCNEGKKEVDCQGKSLDSVPSGIPADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKLTNLQTLSLSTNQLQSVPHGAFDRLGKLQTITLFGNQFDCSRCEILYLSQWIRENSNKVKDGTGQNLHESPDGVTCSDGKVVRTVTNETLKYEC 246
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeehhh.eee..................eee.....................eee.....................eee.....................eee.....................eee.....................eee.....................eee...........hhhhhhhhhhhhhhhh..-------.hhhhh......hhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m19 A   3 CETVTGCTCNEGKKEVDCQGKSLDSVPSGIPADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKLTNLQTLSLSTNQLQSVPHGAFDRLGKLQTITLFGNQFDCSRCEILYLSQWIRENSNKVKD-------ESPDGVTCSDGKVVRTVTNETLKYEC 246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212|      222       232       242    
                                                                                                                                                                                                                                            213     221                         


Chain B from PDB  Type:PROTEIN  Length:237
 aligned with C7B6Z3_PETMA | C7B6Z3 from UniProtKB/TrEMBL  Length:250

    Alignment length:244
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    
         C7B6Z3_PETMA     3 CETVTGCTCNEGKKEVDCQGKSLDSVPSGIPADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKLTNLQTLSLSTNQLQSVPHGAFDRLGKLQTITLFGNQFDCSRCEILYLSQWIRENSNKVKDGTGQNLHESPDGVTCSDGKVVRTVTNETLKYEC 246
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) LRRNT-3m19B07 B:3-33           ------------------------------------------------------------------------------------------------LRR_8-3m19B01 B:130-190                                      -------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) LRRNT-3m19B08 B:3-33           ------------------------------------------------------------------------------------------------LRR_8-3m19B02 B:130-190                                      -------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------LRR_8-3m19B03 B:130-190                                      -------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------LRR_8-3m19B04 B:130-190                                      -------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------------------------------------------------------------LRR_8-3m19B05 B:130-190                                      -------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) -------------------------------------------------------------------------------------------------------------------------------LRR_8-3m19B06 B:130-190                                      -------------------------------------------------------- Pfam domains (6)
         Sec.struct. author hhhhhh.eee....eee..................eee.....................eee.....................eee.....................eee.....................eee.....................eee.....................eee...........hhhhhhhhhhhhhhhh..-------.hhhhh......hhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m19 B   3 CETVTGCTCNEGKKEVDCQGKSLDSVPSGIPADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKLTNLQTLSLSTNQLQSVPHGAFDRLGKLQTITLFGNQFDCSRCEILYLSQWIRENSNKVKD-------ESPDGVTCSDGKVVRTVTNETLKYEC 246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212|      222       232       242    
                                                                                                                                                                                                                                            213     221
   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 3M19)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M19)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: LRR (77)
(-)
Family: LRR_8 (41)
(-)
Petromyzon marinus (Sea lamprey) (3)
1aLRR_8-3m19B01B:130-190
1bLRR_8-3m19B02B:130-190
1cLRR_8-3m19B03B:130-190
1dLRR_8-3m19B04B:130-190
1eLRR_8-3m19B05B:130-190
1fLRR_8-3m19B06B:130-190
(-)
Clan: no clan defined [family: LRRNT] (22)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3M19)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3m18