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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV EPITOPE-SCAFFOLD 4E10_S0_1EZ3A_002_C
 
Authors :  M. A. Holmes
Date :  19 Jan 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Epitope-Scaffold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. E. Correia, Y. E. Ban, M. A. Holmes, H. Xu, K. Ellingson, Z. Kraft, C. Carrico, E. Boni, D. N. Sather, C. Zenobia, K. Y. Burke, T. Bradley-Hewitt, J. F. Bruhn-Johannsen, O. Kalyuzhniy, D. Baker, R. K. Strong, L. Stamatatos, W. R. Schief
Computational Design Of Epitope-Scaffolds Allows Induction Of Antibodies Specific For A Poorly Immunogenic Hiv Vaccine Epitope.
Structure V. 18 1116 2010
PubMed-ID: 20826338  |  Reference-DOI: 10.1016/J.STR.2010.06.010

(-) Compounds

Molecule 1 - 4E10_S0_1EZ3A_002_C (T246)
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29
    Expression System Strain: BL21(DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTIFICIAL GENE
    Organism Taxid: 32630
    Other Details: THE AUTHOR STATES THAT THE EPITOPE-SCAFFOLD IS BASED ON THE NEURONAL T-SNARE SYNTAXIN-1A (PDB ID 1EZ3)

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1FME2Mod. Amino AcidN-FORMYLMETHIONINE
2SO411Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:89 , ARG A:93 , HOH A:138 , ASN B:110 , GLN B:114 , ARG B:117BINDING SITE FOR RESIDUE SO4 A 133
02AC2SOFTWARELYS A:118 , ARG A:119 , ARG C:16BINDING SITE FOR RESIDUE SO4 A 134
03AC3SOFTWARELYS A:89 , LYS A:92 , ARG A:93BINDING SITE FOR RESIDUE SO4 A 135
04AC4SOFTWAREARG A:1 , GLU A:78 , SER A:85 , ARG A:91BINDING SITE FOR RESIDUE SO4 A 136
05AC5SOFTWARELYS B:89 , ARG B:93 , HOH B:137 , GLN C:114 , ARG C:117BINDING SITE FOR RESIDUE SO4 B 133
06AC6SOFTWAREARG A:16 , LYS B:118 , ARG B:119 , LYS B:122 , HOH B:138BINDING SITE FOR RESIDUE SO4 B 134
07AC7SOFTWAREGLU B:79 , SER B:84 , LYS B:89 , LYS B:92 , ARG B:93BINDING SITE FOR RESIDUE SO4 B 135
08AC8SOFTWAREGLU B:78 , SER B:85 , ASP B:87 , LEU B:88 , ARG B:91BINDING SITE FOR RESIDUE SO4 B 136
09AC9SOFTWAREGLN A:114 , ARG A:117 , HOH A:161 , LYS C:89 , ARG C:93 , SO4 C:135 , HOH C:149BINDING SITE FOR RESIDUE SO4 C 133
10BC1SOFTWAREARG B:16 , LYS C:118 , ARG C:119 , LYS C:122 , HOH C:151BINDING SITE FOR RESIDUE SO4 C 134
11BC2SOFTWARESER C:84 , LYS C:89 , LYS C:92 , ARG C:93 , SO4 C:133BINDING SITE FOR RESIDUE SO4 C 135

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LG7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LG7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LG7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LG7)

(-) Exons   (0, 0)

(no "Exon" information available for 3LG7)

(-) 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:124
                                                                                                                                                            
               SCOP domains d3lg7a_ A: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lg7 A   0 mRDKFMDEFFKQVEEIRQYIDRIAENVEEVARQHQAILASPNPNWFDISQLLWLMADIKETANEVRKKLKEIEQSIEQEEKSSADLKIRKRQHEELERKFREVMKEYNATQQDYRKRARKRNLE 126
                            |        9        19        29        39        49        59        69        79|       92       102       112       122    
                            |                                                                             79|                                           
                            0-FME                                                                          83                                           


Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d3lg7b_ B: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lg7 B   0 mRDKFMDEFFKQVEEIRQYIDRIAENVEEVARQHQAILASPNPNWFDISQLLWLMADIKETANEVRKKLKEIEQSIEQEEKSSADLKIRKRQHEELERKFREVMKEYNATQQDYRKRARKRNLE 126
                            |        9        19        29        39        49        59        69        79|       92       102       112       122    
                            0-FME                                                                         79|                                           
                                                                                                           83                                           


Chain C from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d3lg7c_ C: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lg7 C   1 RDKFMDEFFKQVEEIRQYIDRIAENVEEVARQHQAILASPNPNWFDISQLLWLMADIKETANEVRKKLKEIEQSIEQEESSADLKIRKRQHEELERKFREVMKEYNATQQDYRKRARKRNLE 126
                                    10        20        30        40        50        60        70        84        94       104       114       124  
                                                                                                         79|                                          
                                                                                                          84
   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, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LG7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LG7)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3LG7)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3lef 3lf6 3lf9 3lh2 3lhp