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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF A T-BOX RIBOSWITCH STEM I DOMAIN IN COMPLEX WITH ITS COGNATE TRNA
 
Authors :  J. Zhang, A. R. Ferre-D'Amare
Date :  21 Jun 13  (Deposition) - 31 Jul 13  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Riboswitch Mrna, Trna-Mrna Complex, Gene Expression Regulation, Bacteria, Ribosomal Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhang, A. R. Ferre-D'Amare
Co-Crystal Structure Of A T-Box Riboswitch Stem I Domain In Complex With Its Cognate Trna.
Nature V. 500 363 2013
PubMed-ID: 23892783  |  Reference-DOI: 10.1038/NATURE12440

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN YBXF
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RPLGB, YBAB, YBXF, BSU01090
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168
 
Molecule 2 - TRNA-GLY
    Chains: B, E
    Engineered: YES
    Organism Scientific: OCEANOBACILLUS IHEYENSIS
    Organism Taxid: 182710
    Other Details: IN VITRO TRANSCRIPTION USING T7 RNA POLYMERASE
    Synthetic: YES
 
Molecule 3 - T-BOX RIBOSWITCH STEM I
    Chains: C, F
    Engineered: YES
    Organism Scientific: OCEANOBACILLUS IHEYENSIS
    Organism Taxid: 182710
    Other Details: IN VITRO TRANSCRIPTION USING T7 RNA POLYMERASE
    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  (3, 90)

Asymmetric Unit (3, 90)
No.NameCountTypeFull Name
1MG7Ligand/IonMAGNESIUM ION
2MSE4Mod. Amino AcidSELENOMETHIONINE
3SR79Ligand/IonSTRONTIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SR-1Ligand/IonSTRONTIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SR-1Ligand/IonSTRONTIUM ION

(-) Sites  (60, 60)

Asymmetric Unit (60, 60)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH B:201 , HOH B:204BINDING SITE FOR RESIDUE SR B 102
02AC2SOFTWAREU B:54BINDING SITE FOR RESIDUE SR B 103
03AC3SOFTWAREG B:69 , SR B:114BINDING SITE FOR RESIDUE SR B 104
04AC4SOFTWAREU B:19BINDING SITE FOR RESIDUE SR B 105
05AC5SOFTWAREG B:7 , G B:48BINDING SITE FOR RESIDUE SR B 109
06AC6SOFTWAREG B:44BINDING SITE FOR RESIDUE SR B 111
07AC7SOFTWAREG B:38 , HOH B:205 , HOH B:206BINDING SITE FOR RESIDUE SR B 112
08AC8SOFTWARESR B:104BINDING SITE FOR RESIDUE SR B 114
09AC9SOFTWAREC B:62 , G B:63BINDING SITE FOR RESIDUE SR B 115
10BC1SOFTWAREA B:20 , G B:45BINDING SITE FOR RESIDUE SR B 116
11BC2SOFTWAREG B:50 , G B:51BINDING SITE FOR RESIDUE SR B 117
12BC3SOFTWAREG B:63BINDING SITE FOR RESIDUE SR B 118
13BC4SOFTWAREU B:31 , U B:32BINDING SITE FOR RESIDUE SR B 119
14BC5SOFTWAREG B:43 , G B:44BINDING SITE FOR RESIDUE SR B 120
15BC6SOFTWAREG B:63BINDING SITE FOR RESIDUE SR B 121
16BC7SOFTWAREA B:9 , G B:10BINDING SITE FOR RESIDUE SR B 122
17BC8SOFTWAREC B:27 , G B:42BINDING SITE FOR RESIDUE SR B 123
18BC9SOFTWAREG C:59 , HOH C:304 , HOH C:305 , HOH C:306BINDING SITE FOR RESIDUE SR C 201
19CC1SOFTWAREG C:97BINDING SITE FOR RESIDUE SR C 202
20CC2SOFTWAREG C:12BINDING SITE FOR RESIDUE SR C 203
21CC3SOFTWAREHOH C:308BINDING SITE FOR RESIDUE SR C 204
22CC4SOFTWAREU C:55 , G C:59BINDING SITE FOR RESIDUE SR C 205
23CC5SOFTWAREG C:18BINDING SITE FOR RESIDUE SR C 206
24CC6SOFTWAREG C:28 , U C:30BINDING SITE FOR RESIDUE SR C 210
25CC7SOFTWAREA C:39 , C C:102BINDING SITE FOR RESIDUE SR C 211
26CC8SOFTWAREG C:43 , HOH C:301 , HOH C:302 , HOH C:303BINDING SITE FOR RESIDUE SR C 213
27CC9SOFTWAREG C:43BINDING SITE FOR RESIDUE SR C 214
28DC1SOFTWAREU C:37 , G C:38 , G C:70BINDING SITE FOR RESIDUE SR C 216
29DC2SOFTWAREG C:74BINDING SITE FOR RESIDUE SR C 217
30DC3SOFTWAREU C:4 , G C:5BINDING SITE FOR RESIDUE SR C 218
31DC4SOFTWAREG C:2BINDING SITE FOR RESIDUE SR C 219
32DC5SOFTWAREA C:26BINDING SITE FOR RESIDUE SR C 221
33DC6SOFTWAREG C:20BINDING SITE FOR RESIDUE MG C 224
34DC7SOFTWAREG C:28 , A C:29BINDING SITE FOR RESIDUE MG C 225
35DC8SOFTWAREG E:52 , HOH E:201 , HOH E:204BINDING SITE FOR RESIDUE SR E 101
36DC9SOFTWAREG E:44BINDING SITE FOR RESIDUE SR E 102
37EC1SOFTWAREG E:38BINDING SITE FOR RESIDUE SR E 103
38EC2SOFTWAREG E:39 , U E:40BINDING SITE FOR RESIDUE SR E 109
39EC3SOFTWAREG E:7 , G E:48BINDING SITE FOR RESIDUE SR E 110
40EC4SOFTWAREU E:11 , U E:12BINDING SITE FOR RESIDUE SR E 111
41EC5SOFTWAREC E:30 , U E:32BINDING SITE FOR RESIDUE SR E 112
42EC6SOFTWAREA E:9 , G E:10 , U E:11BINDING SITE FOR RESIDUE SR E 114
43EC7SOFTWAREU E:19 , G E:21BINDING SITE FOR RESIDUE SR E 115
44EC8SOFTWAREA E:14 , A E:20 , G E:21BINDING SITE FOR RESIDUE MG E 116
45EC9SOFTWAREA F:39 , A F:60 , C F:102 , SR F:219BINDING SITE FOR RESIDUE SR F 201
46FC1SOFTWAREG F:97BINDING SITE FOR RESIDUE SR F 202
47FC2SOFTWAREG F:43 , HOH F:301BINDING SITE FOR RESIDUE SR F 203
48FC3SOFTWAREU F:55 , G F:59BINDING SITE FOR RESIDUE SR F 204
49FC4SOFTWAREA F:11BINDING SITE FOR RESIDUE SR F 205
50FC5SOFTWAREG F:59BINDING SITE FOR RESIDUE SR F 206
51FC6SOFTWAREG F:45 , A F:46BINDING SITE FOR RESIDUE SR F 207
52FC7SOFTWAREG F:43BINDING SITE FOR RESIDUE SR F 209
53FC8SOFTWAREU F:37 , G F:38 , G F:70BINDING SITE FOR RESIDUE SR F 210
54FC9SOFTWAREU F:50 , A F:51BINDING SITE FOR RESIDUE SR F 215
55GC1SOFTWAREG F:18BINDING SITE FOR RESIDUE SR F 216
56GC2SOFTWAREG F:74 , U F:75BINDING SITE FOR RESIDUE SR F 217
57GC3SOFTWAREA F:71 , U F:72BINDING SITE FOR RESIDUE SR F 218
58GC4SOFTWAREG F:38 , A F:39 , A F:46 , C F:102 , SR F:201BINDING SITE FOR RESIDUE SR F 219
59GC5SOFTWAREU F:21BINDING SITE FOR RESIDUE MG F 220
60GC6SOFTWAREA F:54BINDING SITE FOR RESIDUE MG F 221

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LCK)

(-) 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
                 4lck A   2 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSmVESmKKLGKACGIEVGAAAVAIIL  82
                                    11        21        31        41        51      | 61|       71        81 
                                                                                   58-MSE                    
                                                                                       62-MSE                


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


Chain C from PDB  Type:RNA  Length:102
                                                                                                                                      
                 4lck 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
                 4lck D   2 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSmVESmKKLGKACGIEVGAAAVAIIL  82
                                    11        21        31        41        51      | 61|       71        81 
                                                                                   58-MSE                    
                                                                                       62-MSE                


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


Chain F from PDB  Type:RNA  Length:102
                                                                                                                                      
                 4lck F   1 GGGUGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCACCC 102
                                    10        20        30        40        50        60        70        80        90       100
   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  (0, 0)

(no "SCOP Domain" information available for 4LCK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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        RXL7_BACSU | P46350: 3v7e 4tzp 4tzv 4tzw 4tzz

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