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(-) Description

Title :  STRUCTURE OF A GUIDERNA-BINDING PROTEIN COMPLEX BOUND TO A GRNA
 
Authors :  M. A. Schumacher, E. Karamooz, A. Zikova, L. Trantirek, J. Lukes
Date :  30 Mar 06  (Deposition) - 05 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.37
Chains :  Asym./Biol. Unit :  A,D,R,S
Keywords :  Guide Rna; Krna Editing; Rna Binding Protein, Translation-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, E. Karamooz, A. Zikova, L. Trantirek, J. Lukes
Crystal Structures Of T. Brucei Mrp1/Mrp2 Guide-Rna Binding Complex Reveal Rna Matchmaking Mechanism.
Cell(Cambridge, Mass. ) V. 126 701 2006
PubMed-ID: 16923390  |  Reference-DOI: 10.1016/J.CELL.2006.06.047

(-) Compounds

Molecule 1 - GUIDE RNA 40-MER
    Chains: R
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - RNA TETRAMER
    Chains: S
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - MITOCHONDRIAL RNA-BINDING PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID, COEXPRESSION
    Gene: MRP1
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 185431
    Strain: TREU927
    Synonym: MRP2, GUIDE RNA-BINDING PROTEIN
 
Molecule 4 - MITOCHONDRIAL RNA-BINDING PROTEIN 1
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID, COEXPRESSION
    Gene: MRP2
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 185431
    Strain: TREU927
    Synonym: MRP1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ADRS

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2GJE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GJE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GJE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GJE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GJE)

(-) Exons   (0, 0)

(no "Exon" information available for 2GJE)

(-) 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:145
 aligned with Q952G2_9TRYP | Q952G2 from UniProtKB/TrEMBL  Length:224

    Alignment length:157
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
         Q952G2_9TRYP    65 RARRAQLPPAFDVVHWNDEDISRGHLLRVLHRDTFVVLDYHRQARMLTEEGNKAERVVSVMLPAVYTARFLAVLEGRSEKVEVHSRYTNATFTPNPAAPYTFTLKCTSTRPAQQKQQVAGEEGDETFEWTVEFDVAESLMLQRFLTQALHYNTGFAR 221
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..eeeeee....hhhh.eeeeeee...eeeeeeeee..........eeeeeeeeee.hhhhhhhhhhh.....eeeee..eeeeeee.......eeeeeee...------------...eeeeeeehhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gje A  65 RARRAQLPPAFDVVHWNDEDISRGHLLRVLHRDTFVVLDYHRQARmLTEEGNKAERVVSVmLPAVYTARFLAVLEGRSEKVEVHSRYTNATFTPNPAAPYTFTLKCTSTRP------------DETFEWTVEFDVAESLmLQRFLTQALHYNTGFAR 221
                                    74        84        94       104     | 114       124|      134       144       154       164       174|        -   |   194       204       214       
                                                                       110-MSE        125-MSE                                           175          188             204-MSE             


Chain D from PDB  Type:PROTEIN  Length:147
 aligned with P90629_9TRYP | P90629 from UniProtKB/TrEMBL  Length:206

    Alignment length:147
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       
         P90629_9TRYP    27 QSLPKFEIHDVRDDPALGTMTRVAVDGKLLLISQYPQLGPRKVDPNDLSPQFDADRRISVRLRHVDLAYLVGVCKERVPRHRMETKAYTLDFEKSAQGYHLHGKVHRVASQRMEDWSVKFDNHFAVTLEHFLESALDESFGFRQHYA 173
               SCOP domains -d2gjed1 D:28-173 GBP21                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhh.eeeeeeee..eeeeeeee.....................eeee.hhhhhhhhhhhhh....eeeee....eeeeeee..eeeeeeee........eeeeeeeehhhhhhhhhhhhhhhhhh.hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gje D  27 QSLPKFEIHDVRDDPAEGTmTRVAVDGKLLLISQYPQLGPRKVDPNDLSPQFDADRRISVRLRHVDLAYLVGVCKERVPRHRmETKAYTLDFEKSAQGYHLHGKVHRVASQRmEDWSVKFDNHFAVTLEHFLESALDESFGFRQHYA 173
                                    36        46        56        66        76        86        96       106  |    116       126       136  |    146       156       166       
                                              46-MSE                                                        109-MSE                       139-MSE                              


Chain R from PDB  Type:RNA  Length:13
                                             
                 2gje R  11 UAAAUAACCUGUA  23
                                    20   


Chain S from PDB  Type:RNA  Length:5
                                     
                 2gje S  40 UAGUG  44
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GJE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GJE)

(-) Gene Ontology  (6, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q952G2_9TRYP | Q952G2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
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   (P90629_9TRYP | P90629)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
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
        P90629_9TRYP | P90629: 2gia 2gid
        Q952G2_9TRYP | Q952G2: 2gia 2gid

(-) Related Entries Specified in the PDB File

2gia 2gid