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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 :  12 Apr 11  (Deposition) - 09 Nov 11  (Release) - 18 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
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 - BB_2CX5_001
    Chains: A, B
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:118 , ALA A:150 , VAL A:152 , HOH A:196BINDING SITE FOR RESIDUE GOL A 3731
2AC2SOFTWAREPRO B:105 , HIS B:108 , PRO B:111 , LEU B:112 , THR B:148 , HOH B:181BINDING SITE FOR RESIDUE SO4 B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RI0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RI0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RI0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RI0)

(-) Exons   (0, 0)

(no "Exon" information available for 3RI0)

(-) 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: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 d3ri0a_ A: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh......eee......hhhhhhhhh..hhh.eeeeeeee....eeeeeee.....hhhhhhhhhh...ee.hhhhhhhhhh................eeee.hhhhh..eeee.....eeeeehhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ri0 A   3 LSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLAYGGSKGAYLFLVSGKNRLDLGKAARLVGTDLLELDKWAVAALTGFAAGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      


Chain B from PDB  Type:PROTEIN  Length:155
 aligned with Q5SHN1_THET8 | Q5SHN1 from UniProtKB/TrEMBL  Length:158

    Alignment length:157
                                                                                                                                                                                     158 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     | 
         Q5SHN1_THET8     3 LSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG-   -
               SCOP domains d3ri0b_ B: automated matche  s                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......ee...--.hhhhhhhhh..hhh.eeeeeeee.....eeeeee.....hhhhhhhhhh...ee.hhhhhhhhhh................eeee.hhhhh..eeee.....eeeeehhhhhhhhhh.eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ri0 B   3 LSPSARRVQGALETRGFGHLKVVELPA--RTAKEAAQAVGAEVGQIVKSLAYGGSKGAYLFLVSGKNRLDLGKAARLVGTDLLELDKWAVAALTGFAAGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEGL 159
                                    12        22      | 32        42        52        62        72        82        92       102       112       122       132       142       152       
                                                     29 32
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RI0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RI0)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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: 3rij
UniProtKB/TrEMBL
        Q5SHN1_THET8 | Q5SHN1: 2cx5 2z0k 2z0x

(-) Related Entries Specified in the PDB File

3rfn 3rhu 3rij