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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ASC-BINDING NANOBODY IN COMPLEX WITH THE CARD DOMAIN OF ASC
 
Authors :  A. Lu, F. I. Schmidt, J. Ruan, C. Tang, H. Wu, H. L. Ploegh
Date :  23 Dec 15  (Deposition) - 06 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.21
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Vhh Nanobody, Asc-Binding, Antibody Fragment, Inflammasome, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. I. Schmidt, A. Lu, J. W. Chen, J. Ruan, C. Tang, H. Wu, H. L. Ploegh
A Single Domain Antibody Fragment That Recognizes The Adaptor Asc Defines The Role Of Asc Domains In Inflammasome Assembly.
J. Exp. Med. V. 213 771 2016
PubMed-ID: 27069117  |  Reference-DOI: 10.1084/JEM.20151790

(-) Compounds

Molecule 1 - VHH NANOBODY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844
 
Molecule 2 - APOPTOSIS-ASSOCIATED SPECK-LIKE PROTEIN CONTAINING A CARD
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PYCARD, ASC, CARD5, TMS1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HASC,CASPASE RECRUITMENT DOMAIN-CONTAINING PROTEIN 5,PYD AND CARD DOMAIN-CONTAINING PROTEIN,TARGET OF METHYLATION-INDUCED SILENCING 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5H8O)

(-) Sites  (0, 0)

(no "Site" information available for 5H8O)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:24 -A:98

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:77 -Lys A:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H8O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H8O)

(-) Exons   (0, 0)

(no "Exon" information available for 5H8O)

(-) 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:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee........eeeeee..eeeeee......eee........eeeee....eeeeee.........eeeeee..ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5h8o A   3 QVQLQESGGGLVQPGGSLKLSCAASGFTFSRYAMSWYRQERESVARISSGGGTIYYADSVKGRFTISREDAKNTVYLQMNSLKPEDTAVYYCYVGGFWGQGTQVTVS 113
                                    12        22        32        46        56        66        76        86        96       106       
                                                                 41|                                                                   
                                                                  46                                                                   


Chain B from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5h8o B 115 IDQHRAALIARVTNVEWLLDALYGKQAVRAEPTNPSKMRKLFSFTPAWNWTCKDLLLQALRESQSYLVEDLERS 195
                                   124       134    || 151       161       171       181       191    
                                                  139|                                                
                                                   147
   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 5H8O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H8O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H8O)

(-) Gene Ontology  (72, 72)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:77 - Lys A:78   [ RasMol ]  
 

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  5h8o
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 Related Entries

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

UniProtKB/Swiss-Prot
        ASC_HUMAN | Q9ULZ3: 1ucp 2kn6 3j63

(-) Related Entries Specified in the PDB File

5h8d 5H8D CONTAINS THE VHH ALONE STRUCTURE AT HIGHER RESOLUTION.