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(-) Description

Title :  DESIGN OF A BINDING SCAFFOLD BASED ON VARIABLE LYMPHOCYTE RECEPTORS OF JAWLESS VERTEBRATES BY MODULE ENGINEERING
 
Authors :  H. J. Kim, H. K. Cheong, Y. H. Jeon
Date :  06 Apr 11  (Deposition) - 14 Mar 12  (Release) - 14 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lrr, Protein Binding, Plasma (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Lee, K. Park, J. Han, J. J. Lee, H. J. Kim, S. Hong, W. Heu, Y. J. Kim, J. S. Ha, S. G. Lee, H. K. Cheong, Y. H. Jeon, D. Kim, H. S. Kim
Design Of A Binding Scaffold Based On Variable Lymphocyte Receptors Of Jawless Vertebrates By Module Engineering
Proc. Natl. Acad. Sci. Usa V. 109 3299 2012
PubMed-ID: 22328160  |  Reference-DOI: 10.1073/PNAS.1113193109

(-) Compounds

Molecule 1 - INTERNALIN B, REPEAT MODULES, VARIABLE LYMPHOCYTE RECEPTOR B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: INSHORE HAGFISH
    Organism Scientific: LISTERIA MONOCYTOGENES, SYNTHETIC, EPTATRETUS BURGERI
    Organism Taxid: 637381, 32630, 7764
    Other Details: CHIMERA OF INTERNALIN B, REPEAT MODULES, VARIABLE LYMPHOCYTE RECEPTOR B
    Strain: 08-5923

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:292 , HOH A:335 , HOH A:387 , HOH A:388 , HOH A:389 , HOH B:366BINDING SITE FOR RESIDUE MG A 302
2AC2SOFTWAREHOH A:373 , HOH B:278 , HOH B:352 , HOH B:363 , HOH B:364 , HOH B:365BINDING SITE FOR RESIDUE MG B 301

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:219 -A:252
2A:221 -A:264
3B:219 -B:252
4B:221 -B:264

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Cys A:221 -Pro A:222
2Cys B:221 -Pro B:222

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RFS)

(-) 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:263
 aligned with Q4G1L3_EPTBU | Q4G1L3 from UniProtKB/TrEMBL  Length:305

    Alignment length:263
                                                1                   22   23       32    33           46 47    53 54                                                                                                                                                                                
                                     -         -|       10        20 |    | 26     |   - |      41    |  |49   |  | 57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227   
         Q4G1L3_EPTBU     - --------------------MKFALRGTCVLLALLLCCRNGK----ACPSRCSCSG-----TTVECYSQGRTSVP--TGIPAQT--TYLDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQLKELALNTNQLQSLPDGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWDCTCPGIRYLSEWINKHSGVVRNSAGSVAPDSAKCSGSGKPVRSIIC 230
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhh.hhhhhhhhhhhhh......eehhhhhh...eee..........hhhhh....eee........hhhhh......eee.....................eee.....................eee.....................eee.....................eee.....................eee............hhhhhhhhhhhhhhh.......hhhhh.......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rfs A   2 TITVSTPIKQIFPDDAFAETIKANLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWDCTCPGIRYLSEWINKHSGVVRNSAGSVAPDSAKCSGSGKPVRSIIC 264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with Q4G1L3_EPTBU | Q4G1L3 from UniProtKB/TrEMBL  Length:305

    Alignment length:263
                                                1                   22   23       32    33           46 47    53 54                                                                                                                                                                                
                                     -         -|       10        20 |    | 26     |   - |      41    |  |49   |  | 57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227   
         Q4G1L3_EPTBU     - --------------------MKFALRGTCVLLALLLCCRNGK----ACPSRCSCSG-----TTVECYSQGRTSVP--TGIPAQT--TYLDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQLKELALNTNQLQSLPDGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWDCTCPGIRYLSEWINKHSGVVRNSAGSVAPDSAKCSGSGKPVRSIIC 230
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhh.hhhhhhhhhhhhh......eehhhhhh...eee..........hhhhh....eee........hhhhhhh....eee.....................eee.....................eee.....................eee.....................eee.....................eee............hhhhhhhhhhhhhhh.......hhhhh.......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rfs B   2 TITVSTPIKQIFPDDAFAETIKANLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWDCTCPGIRYLSEWINKHSGVVRNSAGSVAPDSAKCSGSGKPVRSIIC 264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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 3RFS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q4G1L3_EPTBU | Q4G1L3)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q4G1L3_EPTBU | Q4G1L3: 4j4l
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        Q4G1L3_EPTBU | Q4G1L3: 2o6s 3a79 4uip

(-) Related Entries Specified in the PDB File

3rfj