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(-) Description

Title :  AS GROWN, UNTREATED CO-CRYSTALS OF THE TERNARY COMPLEX CONTAINING A T-BOX STEM I RNA, ITS COGNATE TRNAGLY, AND B. SUBTILIS YBXF PROTEIN
 
Authors :  J. Zhang, A. R. Ferre-D'Amare
Date :  10 Jul 14  (Deposition) - 10 Sep 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  8.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Rna, Riboswitch, T-Box, Trna, Ribosomal Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhang, A. R. Ferre-D'Amare
Dramatic Improvement Of Crystals Of Large Rnas By Cation Replacement And Dehydration.
Structure V. 22 1363 2014
PubMed-ID: 25185828  |  Reference-DOI: 10.1016/J.STR.2014.07.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOME-ASSOCIATED PROTEIN L7AE-LIKE
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: RPLGB, YBAB, YBXF, BSU01090
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
 
Molecule 2 - ENGINEERED TRNA
    Chains: B, E
    Engineered: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synthetic: YES
 
Molecule 3 - GLYQ T-BOX STEM I
    Chains: C, F
    Engineered: YES
    Organism Scientific: OCEANOBACILLUS IHEYENSIS
    Organism Taxid: 182710
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4TZP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TZP)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TZP)

(-) 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:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh...eeehhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh..eeee..hhhhhhhhh......eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 4tzp A   2 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSmVESmKKLGKACGIEVGAAAVAIIL  82
                                    11        21        31        41        51      | 61|       71        81 
                                                                                   58-MSE                    
                                                                                       62-MSE                


Chain B from PDB  Type:RNA  Length:70
                                                                                                      
                 4tzp B   5 GAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUCGGGCCCC  79
                                    14        24        34        44        54        64      ||79
                                                                                             71|  
                                                                                              77  


Chain C from PDB  Type:RNA  Length:102
                                                                                                                                      
                 4tzp C   1 GGGUGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCACCC 102
                                    10        20        30        40        50        60        70        80        90       100  


Chain D from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeehhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhh......eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 4tzp D   2 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSmVESmKKLGKACGIEVGAAAVAIIL  82
                                    11        21        31        41        51      | 61|       71        81 
                                                                                   58-MSE                    
                                                                                       62-MSE                


Chain E from PDB  Type:RNA  Length:75
                                                                                                           
                 4tzp E   5 GAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUCGGGCGAAAGCCC  79
                                    14        24        34        44        54        64        74     


Chain F from PDB  Type:RNA  Length:102
                                                                                                                                      
                 4tzp F   1 GGGUGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCACCC 102
                                    10        20        30        40        50        60        70        80        90       100
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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 4TZP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RXL7_BACSU | P46350: 3v7e 4lck 4tzv 4tzw 4tzz

(-) Related Entries Specified in the PDB File

4lck 4LCK CONTAINS THE SAME COMPLEX BUT SUBJECTED TO POST- CRYSTALLIZATION TREATMENTS
4tzv
4tzw
4tzx
4tzy
4tzz