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(-) Description

Title :  CO-CRYSTALS OF THE TERNARY COMPLEX CONTAINING A T-BOX STEM I RNA, ITS COGNATE TRNAGLY, AND B. SUBTILIS YBXF PROTEIN, TREATED BY REMOVING LITHIUM SULFATE AND REPLACING MG2+ WITH SR2+ POST CRYSTALLIZATION
 
Authors :  J. Zhang, A. R. Ferre-D'Amare
Date :  11 Jul 14  (Deposition) - 10 Sep 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.67
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rna, Riboswitch, Trna, T-Box, 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
    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
    Engineered: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synthetic: YES
 
Molecule 3 - T-BOX STEM I
    Chains: C
    Engineered: YES
    Organism Scientific: OCEANOBACILLUS IHEYENSIS HTE831
    Organism Taxid: 221109
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 38)

Asymmetric/Biological Unit (2, 38)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SR36Ligand/IonSTRONTIUM ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG B:43 , SR B:112binding site for residue SR B 104
02AC2SOFTWAREG B:50 , G B:51binding site for residue SR B 105
03AC3SOFTWAREU B:54binding site for residue SR B 106
04AC4SOFTWAREG B:41 , G B:42binding site for residue SR B 108
05AC5SOFTWAREU B:8 , A B:9binding site for residue SR B 110
06AC6SOFTWAREG B:52 , A B:57binding site for residue SR B 111
07AC7SOFTWAREG B:44 , SR B:104binding site for residue SR B 112
08AC8SOFTWAREG B:33binding site for residue SR B 113
09AC9SOFTWAREA B:37binding site for residue SR B 115
10AD1SOFTWAREG C:43binding site for residue SR C 201
11AD2SOFTWAREA C:39 , U C:40 , C C:102 , SR C:221binding site for residue SR C 202
12AD3SOFTWAREG C:59 , SR C:214binding site for residue SR C 203
13AD4SOFTWAREG C:52 , G C:53binding site for residue SR C 204
14AD5SOFTWAREA C:11binding site for residue SR C 205
15AD6SOFTWAREG C:7 , G C:97binding site for residue SR C 206
16AD7SOFTWAREU C:50binding site for residue SR C 208
17AD8SOFTWAREA C:17 , G C:18binding site for residue SR C 209
18AD9SOFTWAREA C:8 , U C:9binding site for residue SR C 211
19AE1SOFTWAREG C:15binding site for residue SR C 213
20AE2SOFTWAREG C:59 , SR C:203binding site for residue SR C 214
21AE3SOFTWAREC C:79binding site for residue SR C 218
22AE4SOFTWAREU C:40 , U C:41binding site for residue SR C 219
23AE5SOFTWAREA C:16 , A C:17 , A C:90binding site for residue SR C 220
24AE6SOFTWAREA C:39 , C C:102 , SR C:202binding site for residue SR C 221

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TZW)

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


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


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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  RXL7_BACSU | P46350
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4lck 4LCK CONTAINS CO-CRYSTALS FULLY TREATED BY CONCURRENT ION EXCHANGE AND DEHYDRATION
4tzp 4TZP CONTAIN UNTREATED, AS GROWN CO-CRYSTALS OF THE T-BOX TERNARY COMPLEX
4tzv 4TZV CONTAINS CO-CRYSTALS THAT WAS SUBJECTED TO REMOVAL OF LITHIUM SULFATE
4tzx
4tzy
4tzz