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(-) Description

Title :  20A MUTANT C-DI-GMP VC2 RIBOSWITCH BOUND WITH 3',3'-CGAMP
 
Authors :  A. M. Ren, D. J. Patel, R. K. Rajashankar
Date :  18 Feb 15  (Deposition) - 15 Apr 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  P,R
Keywords :  Riboswitch, 3', 3'-Cgamp, Spinach, Rna Structure, C-Di-Gmp, Rna-Rna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ren, X. C. Wang, C. A. Kellenberger, K. R. Rajashankar, R. A. Jones, M. C. Hammond, D. J. Patel
Structural Basis For Molecular Discrimination By A 3', 3'-Cgamp Sensing Riboswitch.
Cell Rep V. 11 1 2015
PubMed-ID: 25818298  |  Reference-DOI: 10.1016/J.CELREP.2015.03.004

(-) Compounds

Molecule 1 - RNA (91-MER)
    Chains: R
    Engineered: YES
    Expression System: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI)
    Expression System Taxid: 905932
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
 
Molecule 2 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
    Chains: P
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: UNP RESIDUES 7-97
    Gene: SNRPA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: U1A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : PR

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
14BW1Ligand/Ion2-AMINO-9-[(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-9-(6-AMINO-9H-PURIN-9-YL)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECIN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG R:42 , HOH R:203 , HOH R:206 , HOH R:207binding site for residue MG R 101
2AC2SOFTWAREG R:14 , A R:16 , C R:17 , A R:18 , A R:20 , G R:21 , C R:46 , A R:47 , C R:93 , C R:94binding site for residue 4BW R 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YB1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YB1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YB1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YB1)

(-) Exons   (0, 0)

(no "Exon" information available for 4YB1)

(-) 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 P from PDB  Type:PROTEIN  Length:92
                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee......hhhhhhhhhhhhhh....eeeeeee.......eeeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  4yb1 P  7 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVKRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMA 98
                                    16        26        36        46        56        66        76        86        96  


Chain R from PDB  Type:RNA  Length:91
                                                                                                                          
                  4yb1 R  8 GGGCACGCACAGAGCAAACCAUUCGAAAGAGUGGGACGCAAAGCCUCCGGCCUAAACCAUUGCACCUCGGUAGGUAGCGGGGUUACCGAUG 98
                                    17        27        37        47        57        67        77        87        97
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  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 4YB1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YB1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YB1)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  4yb1
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  SNRPA_HUMAN | P09012
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 Related Entries

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

UniProtKB/Swiss-Prot
        SNRPA_HUMAN | P09012: 1aud 1drz 1dz5 1fht 1m5k 1m5o 1m5p 1m5v 1nu4 1oia 1sj3 1sj4 1sjf 1u6b 1urn 1vbx 1vby 1vbz 1vc0 1vc5 1vc6 1zzn 2a3j 2nz4 2oih 2oj3 2u1a 3bo2 3bo3 3bo4 3cul 3cun 3egz 3g8s 3g8t 3g96 3g9c 3hhn 3iin 3irw 3iwn 3k0j 3l3c 3mum 3mur 3mut 3muv 3mxh 3p49 3pgw 3r1h 3r1l 3ucu 3ucz 3ud3 3ud4 3utr 4c4w 4pr6 4prf 4w90 4w92 5ddo 5ddp 5ddq 5ddr 5fj4

(-) Related Entries Specified in the PDB File

4yaz 4yb0