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(-) Description

Title :  CRYSTAL STRUCTURE OF YTHDF1 YTH DOMAIN IN COMPLEX WITH 5MER M6A RNA
 
Authors :  W. Tempel, C. Xu, C. Bountra, C. H. Arrowsmith, A. M. Edwards, J. Min, Str Genomics Consortium (Sgc)
Date :  16 Sep 14  (Deposition) - 12 Nov 14  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Xu, K. Liu, H. Ahmed, P. Loppnau, M. Schapira, J. Min
Structural Basis For The Discriminative Recognition Of N6-Methyladenosine Rna By The Human Yt521-B Homology Domain Family Of Proteins.
J. Biol. Chem. V. 290 24902 2015
PubMed-ID: 26318451  |  Reference-DOI: 10.1074/JBC.M115.680389

(-) Compounds

Molecule 1 - YTH DOMAIN-CONTAINING FAMILY PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21-V2R-PRARE2
    Expression System Taxid: 511693
    Fragment: UNP RESIDUES 365-554
    Gene: YTHDF1, C20ORF21
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DERMATOMYOSITIS ASSOCIATED WITH CANCER PUTATIVE AUTOANTIGEN 1, DACA-1
 
Molecule 2 - RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
16MZ1Mod. NucleotideN6-METHYLADENOSINE-5'-MONOPHOSPHATE
2UNX7Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 4RCJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RCJ)

(-) 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    
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Chain A from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..............eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhhhh....eeeeeee....eeeeeeee.....................eeeeeeeeeeee.hhh....hhhhh..hhhhh....eehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rcj A 365 HPVLEKLKAAHSYNPKEFEWNLKSGRVFIIKSYSEDDIHRSIKYSIWCSTEHGNKRLDSAFRCMSSKGPVYLLFSVNGSGHFCGVAEMKSPVDYGTSAGVWSQDKWKGKFDVQWIFVKDVPNNQLRHIRLENNDNKPVTNSRDTQEVPLEKAKQVLKIISSYKHTTSIFDDFAHYEKRQEEEEVVRKE 552
                                   374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544        


Chain B from PDB  Type:DNA/RNA  Length:5
                                     
                 4rcj B   1 GGaCU   5
                              |  
                              3-6MZ
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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 4RCJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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 Related Entries

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

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        YTHD1_HUMAN | Q9BYJ9: 4rci

(-) Related Entries Specified in the PDB File

4rci 4rcm