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(-) Description

Title :  A COMPLEX OF TWO EDITOSOME PROTEINS AND TWO NANOBODIES
 
Authors :  Y. -J. Park, W. Hol
Date :  09 Jul 11  (Deposition) - 02 Nov 11  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Biol. Unit 2:  A,B,C,D  (1x)
Keywords :  Rna Editing, Editosome, Nanobody, Single Domain Antibody, Vhh, Krepa3, Krepa6, Rna Binding Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. J. Park, E. Pardon, M. Wu, J. Steyaert, W. G. Hol
Crystal Structure Of A Heterodimer Of Editosome Interaction Proteins In Complex With Two Copies Of A Cross-Reacting Nanobody.
Nucleic Acids Res. V. 40 1828 2012
PubMed-ID: 22039098  |  Reference-DOI: 10.1093/NAR/GKR867

(-) Compounds

Molecule 1 - SINGLE DOMAIN ANTIBODY VHH
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSF
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SINGLE DOMAIN ANTIBODY VHH
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844
 
Molecule 2 - RNA-EDITING COMPLEX PROTEIN MP42
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYC
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 247-393
    Gene: KREPA3, TB927.8.620
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
 
Molecule 3 - MP18 RNA EDITING COMPLEX PROTEIN
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYC
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 20-164
    Gene: KREPA6, TB10.70.2090
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD
Biological Unit 2 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3STB)

(-) Sites  (0, 0)

(no "Site" information available for 3STB)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:24 -A:97
2B:24 -B:97

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro D:122 -Pro D:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3STB)

(-) 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:125
                                                                                                                                                             
               SCOP domains d3stba_ A: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeee....eeeeeeee..hhhhheeeeeee......eeeeee.....eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee..ee......hhhhh.ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3stb A   4 VQLQESGGGLVQAGGSLRLSCAASGRTLSSYAMGWFRQAPGKEREFVAAINRSGSTFYADAVKGRFTISRDNAKNTVYLQMNSLKPEDTAAYYCAADRFSPVVPGPIPVNTVDSWGQGTQVTVSS 128
                                    13        23        33        43        53        63        73        83        93       103       113       123     


Chain B from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains d3stbb_ B: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..eeee....eeeeeeeee.hhhhheeeeeee.....eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.eee......hhhhh.ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3stb B   3 QVQLQESGGGLVQAGGSLRLSCAASGRTLSSYAMGWFRQAPGKEREFVAAINRSGSTFYADAVKGRFTISRDNAKNTVYLQMNSLKPEDTAAYYCAADRFSPVVPGPIPVNTVDSWGQGTQVTVSS 128
                                    12        22        32        42        52        62        72        82        92       102       112       122      


Chain C from PDB  Type:PROTEIN  Length:111
 aligned with Q95W13_9TRYP | Q95W13 from UniProtKB/TrEMBL  Length:393

    Alignment length:111
                                   292       302       312       322       332       342       352       362       372       382       392 
         Q95W13_9TRYP   283 AAHWRCVNHCVMLGVVQNIQEGFVFEDKVLQFTLITDFEGPSPGDPDKDFHTVRVFDSDYSSRVKEQLRDGEWFLVTGRLRMVPQYDGSMRKYYHYPVIQVHPGCGSVLKV 393
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeeeeeee..eeeeeeeeeee..........eeeeeeee.hhhhhhhhhhhh....eeeeeeeeeeeeeee....eeeeeeeeee.....eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3stb C 283 AAHWRCVNHCVMLGVVQNIQEGFVFEDKVLQFTLITDFEGPSPGDPDKDFHTVRVFDSDYSSRVKEQLRDGEWFLVTGRLRMVPQYDGSMRKYYHYPVIQVHPGCGSVLKV 393
                                   292       302       312       322       332       342       352       362       372       382       392 


Chain D from PDB  Type:PROTEIN  Length:108
 aligned with Q38B90_TRYB2 | Q38B90 from UniProtKB/TrEMBL  Length:164

    Alignment length:113
                                    29        39        49        59        69        79        89        99       109       119       129   
         Q38B90_TRYB2    20 KSVNSVTLVGVVHDIQSGFVYEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCFGELFSAEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYIQVQPPHGQVAVIHG 132
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeee....eeeeeeeee..ee..-----.ee..eeeeeeeehhhhhhhhhhhh....eeeeeeeee.....hhhhh......eeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3stb D  20 KSVNSVTLVGVVHDIQSGFVYEDAVTQFTLTTTSIDTT-----VVVEKDHHTIRCFGELFSAEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYIQVQPPHGQVAVIHG 132
                                    29        39        49       | -   |    69        79        89        99       109       119       129   
                                                                57    63
   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 3STB)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 16)

Asymmetric Unit(hide GO term definitions)
Chain C   (Q95W13_9TRYP | Q95W13)
molecular function
    GO:0000175    3'-5'-exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
    GO:0016891    endoribonuclease activity, producing 5'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0016556    mRNA modification    The covalent alteration of one or more nucleotides within an mRNA molecule to produce an mRNA molecule with a sequence that differs from that coded genetically.
    GO:0010038    response to metal ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus.
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.

Chain D   (Q38B90_TRYB2 | Q38B90)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0009451    RNA modification    The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0031019    mitochondrial mRNA editing complex    An mRNA editing complex found in the mitochondrion. The best characterized example is that of Trypanosoma brucei, which catalyzes the insertion and deletion of uridylates.
    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

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