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(-) Description

Title :  EPITOPE BACKBONE GRAFTING BY COMPUTATIONAL DESIGN FOR IMPROVED PRESENTATION OF LINEAR EPITOPES ON SCAFFOLD PROTEINS
 
Authors :  M. L. Azoitei, Y. A. Ban, J. P. Julien, S. Bryson, A. Schroeter, O. Kalyuz J. R. Porter, Y. Adachi, D. Baker, E. Szabo, E. F. Pai, W. R. Schief
Date :  13 Apr 11  (Deposition) - 09 Nov 11  (Release) - 18 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Protein Grafting, Flexible Backbone Design, Epitope-Scaffold, Hiv, Immunogen Design, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Azoitei, Y. E. Ban, J. P. Julien, S. Bryson, A. Schroeter, O. Kalyuzhniy, J. R. Porter, Y. Adachi, D. Baker, E. F. Pai, W. R. Schief
Computational Design Of High-Affinity Epitope Scaffolds By Backbone Grafting Of A Linear Epitope.
J. Mol. Biol. V. 415 175 2012
PubMed-ID: 22061265  |  Reference-DOI: 10.1016/J.JMB.2011.10.003

(-) Compounds

Molecule 1 - SC_2CX5
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SEE REMARK 999
    Gene: TTHA1699
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8 / ATCC 27634 / DSM 579

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE C:19 , ALA C:146 , HOH C:442 , ASP D:154 , HOH D:228BINDING SITE FOR RESIDUE GOL C 3731

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RIJ)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RIJ)

(-) 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:157
 aligned with Q5SHN1_THET8 | Q5SHN1 from UniProtKB/TrEMBL  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
         Q5SHN1_THET8     2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
               SCOP domains d3rija_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....eee......hhhhhhhhhh.hhh.eeeeeeeee..eeeeeeee.....hhhhhhhhhh...ee.hhhhhhhhhh................eeee.hhhhh..eeee.....eeeeehhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rij A   2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVYGGEKGAYLFLVSGKNRLDLGKATRLVGGPLLEADKWAVAALTGFDAGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with Q5SHN1_THET8 | Q5SHN1 from UniProtKB/TrEMBL  Length:158

    Alignment length:156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      
         Q5SHN1_THET8     3 LSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
               SCOP domains d3rijb_ B: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh......eee......hhhhhhhhh..hhhh.eeeeeee....eeeeeee.....hhhhhhhhhh...ee.hhhhhhhhhh................eeee.hhhhh..eeee.....eeeeehhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rij B   3 LSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVYGGEKGAYLFLVSGKNRLDLGKATRLVGGPLLEADKWAVAALTGFDAGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      


Chain C from PDB  Type:PROTEIN  Length:150
 aligned with Q5SHN1_THET8 | Q5SHN1 from UniProtKB/TrEMBL  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
         Q5SHN1_THET8     2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
               SCOP domains d3rijc_ C: automated matche       s                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh......eee..-------.............eeeeeee....eeeeeee.....hhhhhhhhhh...ee.hhhhhhh...................eeee.hhh....eeee.....eeeeehhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rij C   2 SLSPSARRVQGALETRGFGHLKVVELP-------EAAQAVGAEVGQIVKSLVYGGEKGAYLFLVSGKNRLDLGKATRLVGGPLLEADKWAVAALTGFDAGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
                                    11        21      |  -    |   41        51        61        71        81        91       101       111       121       131       141       151       
                                                     28      36                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:157
 aligned with Q5SHN1_THET8 | Q5SHN1 from UniProtKB/TrEMBL  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
         Q5SHN1_THET8     2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
               SCOP domains d3rijd_ D: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh......eee......hhhhhhhhh..hhhh.eeeeeee....eeeeeee.....hhhhhhhhhh...ee.hhhhhhhhhh................eeee.hhhhh..eeee.....eeeeehhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rij D   2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVYGGEKGAYLFLVSGKNRLDLGKATRLVGGPLLEADKWAVAALTGFDAGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SHN1_THET8 | Q5SHN1)
molecular function
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
biological process
    GO:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic code.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q5SHN1_THET8 | Q5SHN1: 3ri0
UniProtKB/TrEMBL
        Q5SHN1_THET8 | Q5SHN1: 2cx5 2z0k 2z0x

(-) Related Entries Specified in the PDB File

3rfn 3rhu 3ri0