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(-)Asym./Biol. Unit
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(-) Description

Title :  SPECIFIC RECOGNITION OF A SINGLE-STRANDED RNA SEQUENCE BY AN ENGINEERED SYNTHETIC ANTIBODY FRAGMENT
 
Authors :  H. Huang, D. Qin, N. Li, Y. Shao, J. P. Staley, A. A. Kossiakoff, S. Koide, J. A. Piccirilli
Date :  28 Sep 15  (Deposition) - 21 Sep 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym./Biol. Unit :  H,L,N
Keywords :  Antibody, Fab, Ssrna, Immune System-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shao, H. Huang, D. Qin, N. S. Li, A. Koide, J. P. Staley, S. Koide, A. A. Kossiakoff, J. A. Piccirilli
Specific Recognition Of A Single-Stranded Rna Sequence By A Synthetic Antibody Fragment.
J. Mol. Biol. V. 428 4100 2016
PubMed-ID: 27593161  |  Reference-DOI: 10.1016/J.JMB.2016.08.029

(-) Compounds

Molecule 1 - FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - RNA
    Chains: N
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5E08)

(-) Sites  (0, 0)

(no "Site" information available for 5E08)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:23 -H:97
2H:154 -H:210
3H:230 -L:215
4L:24 -L:89
5L:135 -L:195

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe H:160 -Pro H:161
2Glu H:162 -Pro H:163
3Asp H:231 -Lys H:232
4Ser L:8 -Pro L:9
5Tyr L:95 -Pro L:96
6Tyr L:141 -Pro L:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E08)

(-) Exons   (0, 0)

(no "Exon" information available for 5E08)

(-) 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 H from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhh.eeeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee.hhhhhhh......ee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e08 H   2 EVQLVESGGGLVQPGGSLRLSCAASGFSISSSYIHWVRQAPGKGLEWVAYIYPYYGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYYSSGGSYYRYSRGFDYWGQGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH 234
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141|      155       165       175       185       195       205       215       225         
                                                                                                                                                                     141|                                                                                        
                                                                                                                                                                      146                                                                                        


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee....eeeeeee.......eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e08 L   1 SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYSYPYTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain N from PDB  Type:RNA  Length:12
                                            
                 5e08 N   1 GUAUGCAUAGGC  12
                                    10
   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 5E08)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E08)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5E08)

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Asymmetric/Biological Unit
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  Sites
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  Cis Peptide Bonds
    Asp H:231 - Lys H:232   [ RasMol ]  
    Glu H:162 - Pro H:163   [ RasMol ]  
    Phe H:160 - Pro H:161   [ RasMol ]  
    Ser L:8 - Pro L:9   [ RasMol ]  
    Tyr L:141 - Pro L:142   [ RasMol ]  
    Tyr L:95 - Pro L:96   [ RasMol ]  
 

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  5e08
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 Related Entries

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