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(-) Description

Title :  CRYSTAL STRUCTURE OF YTH DOMAIN OF ZYGOSACCHAROMYCES ROUXII MRB1 PROTEIN IN COMPLEX WITH N6-METHYLADENOSINE RNA
 
Authors :  S. Luo, L. Tong
Date :  04 Aug 14  (Deposition) - 10 Sep 14  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,O,P,Q,R,S,T
Biol. Unit 1:  A,O  (1x)
Biol. Unit 2:  B,P  (1x)
Biol. Unit 3:  C,Q  (1x)
Biol. Unit 4:  D,T  (1x)
Biol. Unit 5:  E,S  (1x)
Biol. Unit 6:  F,R  (1x)
Keywords :  N6-Methyladenosine Rna, Yth Rna Binding Domain, Rna Binding Protein- Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Luo, L. Tong
Molecular Basis For The Recognition Of Methylated Adenines In Rna By The Eukaryotic Yth Domain.
Proc. Natl. Acad. Sci. Usa V. 111 13834 2014
PubMed-ID: 25201973  |  Reference-DOI: 10.1073/PNAS.1412742111

(-) Compounds

Molecule 1 - ZYRO0G01672P
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28A(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentYTH DOMAIN, UNP RESIDUES 166-329
    GeneZYRO0G01672G
    Organism ScientificZYGOSACCHAROMYCES ROUXII
    Organism Taxid559307
    StrainATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229
 
Molecule 2 - RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')
    ChainsO, P, Q, R, S, T
    EngineeredYES
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Other DetailsN6-METHYLADENOSINE 7-MER RNA
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFOPQRST
Biological Unit 1 (1x)A     O     
Biological Unit 2 (1x) B     P    
Biological Unit 3 (1x)  C     Q   
Biological Unit 4 (1x)   D       T
Biological Unit 5 (1x)    E     S 
Biological Unit 6 (1x)     F   R  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
16MZ6Mod. NucleotideN6-METHYLADENOSINE-5'-MONOPHOSPHATE
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
16MZ1Mod. NucleotideN6-METHYLADENOSINE-5'-MONOPHOSPHATE
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
16MZ1Mod. NucleotideN6-METHYLADENOSINE-5'-MONOPHOSPHATE
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
16MZ1Mod. NucleotideN6-METHYLADENOSINE-5'-MONOPHOSPHATE
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
16MZ1Mod. NucleotideN6-METHYLADENOSINE-5'-MONOPHOSPHATE
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (2, 3)
No.NameCountTypeFull Name
16MZ1Mod. NucleotideN6-METHYLADENOSINE-5'-MONOPHOSPHATE
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 6 (2, 3)
No.NameCountTypeFull Name
16MZ1Mod. NucleotideN6-METHYLADENOSINE-5'-MONOPHOSPHATE
2MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4U8T)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U8T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U8T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U8T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U8T)

(-) Exons   (0, 0)

(no "Exon" information available for 4U8T)

(-) 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:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhh......eeeeeee....eeeeeeeeeeeee...hhhhhh.....eeeeeeeeeeeee.hhh....hhhhh..hhhhh....eehhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u8t A 165 GAIIPPWIHVPDHSRFFVIKSSSLEHVKKSFYNGIWSSTFYGNKRLSEAYESLPQGAKIYLLFSVNASGRFCGVAEmSSNLREDLDTSIWGSRYRHAFKVRWIVVRDVHNRSLKQFLIPANDmKPVTNSRDTQEIPATISKSILKLFKYVQSFLDDD 327
                                   174       184       194       204       214       224       234      |244       254||     266       276       286  |    296       306       320       
                                                                                                      241-MSE       255|                            289-MSE                   315|       
                                                                                                                     258                                                       320       

Chain B from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhh......eeeeeee....eeeeeeee........hhhhhh....eeeeeeeeeeee.hhh....hhhhh..hhhhh....eehhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u8t B 165 GAIIPPWIHVPDHSRFFVIKSSSLEHVKKSFYNGIWSSTFYGNKRLSEAYESLPQGAKIYLLFSVNASGRFCGVAEmSSNLREDLDTSIWGYRHAFKVRWIVVRDVHNRSLKQFLIPANDmKPVTNSRDTQEIPATISKSILKLFKYVQSFLDD 326
                                   174       184       194       204       214       224       234      |244       254||     268       278       288|      298       308      |322    
                                                                                                      241-MSE       255|                          289-MSE                   315|      
                                                                                                                     260                                                     320      

Chain C from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhh......eeeeeee....eeeeeeee........hhhhhh......eeeeeeeeeeee.hhh....hhhhh..hhhhh...eeehhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u8t C 165 GAIIPPWIHVPDHSRFFVIKSSSLEHVKKSFYNGIWSSTFYGNKRLSEAYESLPQGAKIYLLFSVNASGRFCGVAEmSSNLREDLDTSIWGSRYRHAFKVRWIVVRDVHNRSLKQFLIPANDmKPVTNSRDTQEIPATISKSILKLFKYVQSFLD 325
                                   174       184       194       204       214       224       234      |244       254||     266       276       286  |    296       306       320     
                                                                                                      241-MSE       255|                            289-MSE                   315|     
                                                                                                                     258                                                       320     

Chain D from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhh......eeeeeee....eeeeeeee........hhhhhh....eeeeeeeeeeee.hhh....hhhhh..hhhhh....eehhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u8t D 165 GAIIPPWIHVPDHSRFFVIKSSSLEHVKKSFYNGIWSSTFYGNKRLSEAYESLPQGAKIYLLFSVNASGRFCGVAEmSSNLREDLDTSIWGYRHAFKVRWIVVRDVHNRSLKQFLIPANDmKPVTNSRDTQEIPATISKSILKLFKYEQSEVQSFLD 325
                                   174       184       194       204       214       224       234      |244       254||     268       278       288|      298       308       318       
                                                                                                      241-MSE       255|                          289-MSE                                
                                                                                                                     260                                                                 

Chain E from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhhh.....eeeeeee....eeeeeeee........hhhhhh....eeeeeeeeeeee.hhh....hhhhh..hhhhh....eehhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u8t E 165 GAIIPPWIHVPDHSRFFVIKSSSLEHVKKSFYNGIWSSTFYGNKRLSEAYESLPQGAKIYLLFSVNASGRFCGVAEmSSNLREDLDTSIWGYRHAFKVRWIVVRDVHNRSLKQFLIPANDmKPVTNSRDTQEIPATISKSILKLFKYVQSFLD 325
                                   174       184       194       204       214       224       234      |244       254||     268       278       288|      298       308      |322   
                                                                                                      241-MSE       255|                          289-MSE                   315|     
                                                                                                                     260                                                     320     

Chain F from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhh......eeeeeee....eeeeeeee........hhhhhh....eeeeeeeeeeee.hhh....hhhhh..hhhhh...eeehhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u8t F 165 GAIIPPWIHVPDHSRFFVIKSSSLEHVKKSFYNGIWSSTFYGNKRLSEAYESLPQGAKIYLLFSVNASGRFCGVAEmSSNLREDLDTSIWGYRHAFKVRWIVVRDVHNRSLKQFLIPANDmKPVTNSRDTQEIPATISKSILKLFKYVQSFLD 325
                                   174       184       194       204       214       224       234      |244       254||     268       278       288|      298       308      |322   
                                                                                                      241-MSE       255|                          289-MSE                   315|     
                                                                                                                     260                                                     320     

Chain O from PDB  Type:RNA  Length:7
                                       
                 4u8t O  -3 AGGxCAU   3
                               |   
                               0-6MZ

Chain P from PDB  Type:RNA  Length:7
                                       
                 4u8t P  -3 AGGxCAU   3
                               |   
                               0-6MZ

Chain Q from PDB  Type:RNA  Length:7
                                       
                 4u8t Q  -3 AGGxCAU   3
                               |   
                               0-6MZ

Chain R from PDB  Type:RNA  Length:7
                                       
                 4u8t R  -3 AGGxCAU   3
                               |   
                               0-6MZ

Chain S from PDB  Type:RNA  Length:7
                                       
                 4u8t S  -3 AGGxCAU   3
                               |   
                               0-6MZ

Chain T from PDB  Type:RNA  Length:7
                                       
                 4u8t T  -3 AGGxCAU   3
                               |   
                               0-6MZ

   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 4U8T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U8T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U8T)

(-) Gene Ontology  (6, 6)

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