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(-) Description

Title :  VARIABLE LYMPHOCYTE RECEPTOR RECOGNITION OF THE IMMUNODOMINANT GLYCOPROTEIN OF BACILLUS ANTHRACIS SPORES
 
Authors :  R. N. Kirchdoerfer, B. R. Herrin, B. W. Han, C. L. Turnbough Jr. , M. D. Co I. A. Wilson
Date :  21 Sep 11  (Deposition) - 14 Mar 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Leucine-Rich Repeat, Antigen-Binding, Secreted, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. N. Kirchdoerfer, B. R. Herrin, B. W. Han, C. L. Turnbough, M. D. Cooper, I. A. Wilson
Variable Lymphocyte Receptor Recognition Of The Immunodominant Glycoprotein Of Bacillus Anthracis Spores.
Structure V. 20 479 2012
PubMed-ID: 22405006  |  Reference-DOI: 10.1016/J.STR.2012.01.009

(-) Compounds

Molecule 1 - BCLA PROTEIN
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN
    GeneBCLA, BA_1222, GBAA_1222
    MutationYES
    Organism CommonANTHRAX,ANTHRAX BACTERIUM
    Organism ScientificBACILLUS ANTHRACIS
    Organism Taxid1392
    SynonymSPORE SURFACE GLYCOPROTEIN BCLA
 
Molecule 2 - VARIABLE LYMPHOCYTE RECEPTOR B
    ChainsD, E, F
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    FragmentANTIGEN-BINDING DOMAIN
    GeneVLR-B
    Organism CommonMARINE LAMPREY
    Organism ScientificPETROMYZON MARINUS
    Organism Taxid7757

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:108 , VAL A:110 , GLN A:120 , HOH A:361 , VAL D:43 , VAL D:68BINDING SITE FOR RESIDUE GOL A 3
2AC2SOFTWARETHR A:204 , THR B:152 , PRO B:159 , VAL B:160 , GLY B:162 , THR B:163 , GLY B:164 , HOH B:254BINDING SITE FOR RESIDUE GOL B 1
3AC3SOFTWAREPRO D:44 , ALA D:45 , GLY D:46 , ILE D:47 , VAL D:68 , SER D:71BINDING SITE FOR RESIDUE GOL D 2

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1D:22 -D:28
2D:26 -D:35
3D:135 -D:167
4D:137 -D:187
5E:22 -E:28
6E:26 -E:35
7E:135 -E:167
8E:137 -E:187
9F:26 -F:35
10F:137 -F:187

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asn A:185 -Pro A:186
2Asn B:185 -Pro B:186
3Asn C:185 -Pro C:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TWI)

(-) Sequences/Alignments

Asymmetric/Biological 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:136
 aligned with Q81JD7_BACAN | Q81JD7 from UniProtKB/TrEMBL  Length:382

    Alignment length:136
                                                                                                                                                                382 
                                   257       267       277       287       297       307       317       327       337       347       357       367       377    | 
         Q81JD7_BACAN   248 GLGLPAGLYAFNSGGISLDLGINDPVPFNTVGSQFGTAISQLDADTFVISETGFYKITVIANTATASVLGGLTIQVNGVPVPGTGSSLISLGAPIVIQAITQITTTPSLVEVIVTGLGLSLALGTSASIIIEKVA-   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee...eee.........eeeeee...eeeee..eeee...eeeeeeeeee........eeeeee..ee.....ee......eeeeeeeeee....eeeeeeee...eee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3twi A  80 GLGLPAGLYAFNSGGISLDLGINDPVPFNTVGSQFGTAISQLDADTFVISETGFYKITVIANTATASVLGGLTIQVNGVPVPGTGSSLISLGAPIVIQAITQITTNPSLVEVIVTGLGLSLALGTSASIIIEKVAF 215
                                    89        99       109       119       129       139       149       159       169       179       189       199       209      

Chain B from PDB  Type:PROTEIN  Length:136
 aligned with Q81JD7_BACAN | Q81JD7 from UniProtKB/TrEMBL  Length:382

    Alignment length:136
                                                                                                                                                                382 
                                   257       267       277       287       297       307       317       327       337       347       357       367       377    | 
         Q81JD7_BACAN   248 GLGLPAGLYAFNSGGISLDLGINDPVPFNTVGSQFGTAISQLDADTFVISETGFYKITVIANTATASVLGGLTIQVNGVPVPGTGSSLISLGAPIVIQAITQITTTPSLVEVIVTGLGLSLALGTSASIIIEKVA-   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee...eee.........eeeeee...eeeee..eeee...eeeeeeeeee........eeeeee..ee.....ee......eeeeeeeeee....eeeeeeee...eee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3twi B  80 GLGLPAGLYAFNSGGISLDLGINDPVPFNTVGSQFGTAISQLDADTFVISETGFYKITVIANTATASVLGGLTIQVNGVPVPGTGSSLISLGAPIVIQAITQITTNPSLVEVIVTGLGLSLALGTSASIIIEKVAF 215
                                    89        99       109       119       129       139       149       159       169       179       189       199       209      

Chain C from PDB  Type:PROTEIN  Length:136
 aligned with Q81JD7_BACAN | Q81JD7 from UniProtKB/TrEMBL  Length:382

    Alignment length:136
                                                                                                                                                                382 
                                   257       267       277       287       297       307       317       327       337       347       357       367       377    | 
         Q81JD7_BACAN   248 GLGLPAGLYAFNSGGISLDLGINDPVPFNTVGSQFGTAISQLDADTFVISETGFYKITVIANTATASVLGGLTIQVNGVPVPGTGSSLISLGAPIVIQAITQITTTPSLVEVIVTGLGLSLALGTSASIIIEKVA-   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee...eee.........eeeeee...eeeee..eeee...eeeeeeeeee........eeeeee..ee.....ee......eeeeeeeeee....eeeeeeee...eee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3twi C  80 GLGLPAGLYAFNSGGISLDLGINDPVPFNTVGSQFGTAISQLDADTFVISETGFYKITVIANTATASVLGGLTIQVNGVPVPGTGSSLISLGAPIVIQAITQITTNPSLVEVIVTGLGLSLALGTSASIIIEKVAF 215
                                    89        99       109       119       129       139       149       159       169       179       189       199       209      

Chain D from PDB  Type:PROTEIN  Length:168
 aligned with A9Z0I5_PETMA | A9Z0I5 from UniProtKB/TrEMBL  Length:270

    Alignment length:168
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         A9Z0I5_PETMA    21 ACPSQCSCSGTTVNCQERSLASVPAGIPTTTQVLHLYINQITKLEPGVFDSLTQLTYLNLAVNQLTALPVGVFDKLTKLTHLALHINQLKSIPMGVFDNLKSLTHIYLFNNPWDCECSDILYLKNWIVQHASIVNPLGNGGVDNVKCSGTNTPVRAVTEASTSPSKCP 188
               SCOP domains d3twid_ D: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee..eee..................eee.....................eee.....................eee.....................eee.........hhhhhhhhhhhhhhhhhh......hhhhh.......hhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3twi D  21 ACPSQCSCSGTTVNCQERSLASVPAGIPTTTQVLHLYINQITKLEPGVFDSLTQLTYLNLAVNQLTALPVGVFDKLTKLTHLALHINQLKSIPMGVFDNLKSLTHIYLFNNPWDCECSDILYLKNWIVQHASIVNPLGNGGVDNVKCSGTNTPVRAVTEASTSPSKCP 188
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        

Chain E from PDB  Type:PROTEIN  Length:166
 aligned with A9Z0I5_PETMA | A9Z0I5 from UniProtKB/TrEMBL  Length:270

    Alignment length:167
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
         A9Z0I5_PETMA    21 ACPSQCSCSGTTVNCQERSLASVPAGIPTTTQVLHLYINQITKLEPGVFDSLTQLTYLNLAVNQLTALPVGVFDKLTKLTHLALHINQLKSIPMGVFDNLKSLTHIYLFNNPWDCECSDILYLKNWIVQHASIVNPLGNGGVDNVKCSGTNTPVRAVTEASTSPSKC 187
               SCOP domains d3twie1 E:21-185 automated matches                                                                                                                                   -- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee..................eee.....................eee.....................eee.....................eee...........hhhhhhhhhhhhhhhh.....hhhhhh.......hhhhhhhhhh...-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3twi E  21 ACPSQCSCSGTTVNCQERSLASVPAGIPTTTQVLHLYINQITKLEPGVFDSLTQLTYLNLAVNQLTALPVGVFDKLTKLTHLALHINQLKSIPMGVFDNLKSLTHIYLFNNPWDCECSDILYLKNWIVQHASIVNPLGNGGVDNVKCSGTNTPVRAVTEASTSPS-C 187
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    | |
                                                                                                                                                                                              185 |
                                                                                                                                                                                                187

Chain F from PDB  Type:PROTEIN  Length:117
 aligned with A9Z0I5_PETMA | A9Z0I5 from UniProtKB/TrEMBL  Length:270

    Alignment length:164
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183    
         A9Z0I5_PETMA    24 SQCSCSGTTVNCQERSLASVPAGIPTTTQVLHLYINQITKLEPGVFDSLTQLTYLNLAVNQLTALPVGVFDKLTKLTHLALHINQLKSIPMGVFDNLKSLTHIYLFNNPWDCECSDILYLKNWIVQHASIVNPLGNGGVDNVKCSGTNTPVRAVTEASTSPSKC 187
               SCOP domains d3twif  _ F:  aut oma   te   d matches                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......--.ee..-...-...---..---.ee.......---...------..eee.............------..eee......-......------..eee......--...--.h-.hhhhhhhhhh......hhhhh.---...hhhhh-..------. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3twi F  24 SQCSCS--TVNCQ-RSL-SVP---PT---VLHLYINQIT---PGV------LTYLNLAVNQLTALPVGV------LTHLALHINQL-SIPMGV------LTHIYLFNNPW--ECS--LY-KNWIVQHASIVNPLGNGGVDNVK---TNTPVRAV-EA------C 187
                                 |  33  | | | 43|   ||  53        |-  | |    - |      83        |-     | 103     | 113  |    123       133  | |  ||-|      153       163  |   |173   | ||  -   |
                                29 32  36 | | | |  48|  53       62  66 |     75               92     99       109 |  116    123       133  | |  || |                   166 170    177 ||    187
                                         38 | | |   49                 68                                        111                      136 |  || |                                179|       
                                           40 | |                                                                                           138  || |                                 180       
                                             42 |                                                                                              141| |                                           
                                               44                                                                                               142 |                                           
                                                                                                                                                  144                                           

   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  (1, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TWI)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q81JD7_BACAN | Q81JD7)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0050764    regulation of phagocytosis    Any process that modulates the frequency, rate or extent of phagocytosis, the process in which phagocytes engulf external particulate material.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Chain D,E,F   (A9Z0I5_PETMA | A9Z0I5)

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 Related Entries

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

UniProtKB/TrEMBL
        Q81JD7_BACAN | Q81JD72r6q 3tyj

(-) Related Entries Specified in the PDB File

2r6q STRUCTURE OF WILD-TYPE BCLA-CTD
3tyj