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(-) Description

Title :  STRUCTURE OF EDITOSOME PROTEIN
 
Authors :  Y. -J. Park, W. Hol
Date :  03 Feb 12  (Deposition) - 04 Jul 12  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B (1x),C (1x)
Keywords :  Krepa1, Vhh, Single Domain Antibody, Protein Binding, Rna Binding Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. J. Park, T. Budiarto, M. Wu, E. Pardon, J. Steyaert, W. G. Hol
The Structure Of The C-Terminal Domain Of The Largest Editosome Interaction Protein And Its Role In Promoting Rna Binding By Rna-Editing Ligase L2.
Nucleic Acids Res. V. 40 6966 2012
PubMed-ID: 22561373  |  Reference-DOI: 10.1093/NAR/GKS369

(-) Compounds

Molecule 1 - SINGLE DOMAIN ANTIBODY VHH
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSF
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844
 
Molecule 2 - RNA-EDITING COMPLEX PROTEIN MP81
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSF
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:99 , GLU A:113 , ASP A:115 , HOH A:327 , HOH D:801 , HOH D:806BINDING SITE FOR RESIDUE NA A 201
2AC2SOFTWAREASP B:99 , GLU B:113 , ASP B:115 , HOH B:327 , HOH C:805 , HOH C:818BINDING SITE FOR RESIDUE NA B 201

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:22 -A:96
2B:22 -B:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DKA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DKA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DKA)

(-) Exons   (0, 0)

(no "Exon" information available for 4DKA)

(-) 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:127
                                                                                                                                                               
               SCOP domains d4dkaa_ A: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeee....eeeeeeeee.hhhh..eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee........ee.hhhhh.ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dka A   1 QVQLQESGGGLVQAGGSLRLSCAASGRTSSLYSMGWFRQAPGKEREFVAAISRNGANTYYTDSVKGRFTISRDNAKNTVELQMNSLKPEDTAVYYCAADRFPTMEVVTIMTNEYDYWGQGTQVTVSS 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       


Chain B from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains d4dkab_ B: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeee....eeeeeeeee.hhhh..eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee...........hhhhh.ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dka B   1 QVQLQESGGGLVQAGGSLRLSCAASGRTSSLYSMGWFRQAPGKEREFVAAISRNGANTYYTDSVKGRFTISRDNAKNTVELQMNSLKPEDTAVYYCAADRFPTMEVVTIMTNEYDYWGQGTQVTVSS 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       


Chain C from PDB  Type:PROTEIN  Length:86
 aligned with Q95W15_9TRYP | Q95W15 from UniProtKB/TrEMBL  Length:762

    Alignment length:135
                                   636       646       656       666       676       686       696       706       716       726       736       746       756     
         Q95W15_9TRYP   627 SNALMIGRIADVQHGFLGAMTVTQYVLEVDGDERINSKGVTTPASACTPDPASTKAVEAKGEEGEVVEPEKEFIVIRCMGDNFPASLLKDQVKLGSRVLVQGTLRMNRHVDDVSKRLHAYPFIQVVPPLGYVKVV 761
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeee..eeeeeeeeee..--------------------------------------..eeeeeeee.---------.......eeeeeeeee...ee......ee...eeeee--.eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dka C 627 SNALMIGRIADVQHGFLGAMTVTQYVLEVDG--------------------------------------EKEFIVIRCMG---------DQVKLGSRVLVQGTLRMNRHVDDVSKRLHAYPFIQVV--LGYVKVV 761
                                   636       646       656|        -         -         -       696       706       716       726       736       746     | 756     
                                                        657                                    696       706       716                                 752  |      
                                                                                                                                                          755      


Chain D from PDB  Type:PROTEIN  Length:82
 aligned with Q95W15_9TRYP | Q95W15 from UniProtKB/TrEMBL  Length:762

    Alignment length:136
                                   636       646       656       666       676       686       696       706       716       726       736       746       756      
         Q95W15_9TRYP   627 SNALMIGRIADVQHGFLGAMTVTQYVLEVDGDERINSKGVTTPASACTPDPASTKAVEAKGEEGEVVEPEKEFIVIRCMGDNFPASLLKDQVKLGSRVLVQGTLRMNRHVDDVSKRLHAYPFIQVVPPLGYVKVVG 762
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeee..eeeeeeeee.-----------------------------------------..eeeeee.-----------......eeeeeeeee..eee......eee..eeeee--.eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dka D 627 SNALMIGRIADVQHGFLGAMTVTQYVLEV-----------------------------------------KEFIVIRCM-----------QVKLGSRVLVQGTLRMNRHVDDVSKRLHAYPFIQVV--LGYVKVVG 762
                                   636       646        |-         -         -         -         -|       |-         -|      726       736       746     | 756      
                                                      655                                       697     705         717                                752  |       
                                                                                                                                                          755
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DKA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DKA)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain C,D   (Q95W15_9TRYP | Q95W15)
molecular function
    GO:0045294    alpha-catenin binding    Interacting selectively and non-covalently with the alpha subunit of the catenin complex.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0070706    RNA nucleotide deletion    The modification of an RNA molecule by removal of a single nucleotide.
    GO:0070705    RNA nucleotide insertion    The modification of an RNA molecule by insertion of one or more nucleotides.
    GO:1900864    mitochondrial RNA modification    Any RNA modification that takes place in mitochondrion.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/TrEMBL
        Q95W15_9TRYP | Q95W15: 4dk3 4dk6

(-) Related Entries Specified in the PDB File

4dk3 4dk6