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(-) Description

Title :  THE CRYSTAL STRUCTURE OF AN RNA COMPLEX
 
Authors :  W. Tempel, C. Xu, K. Liu, Y. Li, C. Bountra, C. H. Arrowsmith, A. M. Edward Structural Genomics Consortium (Sgc)
Date :  15 Aug 14  (Deposition) - 17 Sep 14  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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, X. Wang, K. Liu, I. A. Roundtree, W. Tempel, Y. Li, Z. Lu, C. He, J. Min
Structural Basis For Selective Binding Of M(6)A Rna By The Ythdc1 Yth Domain.
Nat. Chem. Biol. V. 10 927 2014
PubMed-ID: 25242552  |  Reference-DOI: 10.1038/NCHEMBIO.1654

(-) Compounds

Molecule 1 - YTH DOMAIN-CONTAINING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21-V2R-PRARE2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YTHDC1, KIAA1966, YT521
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PUTATIVE SPLICING FACTOR YT521, YT521-B
 
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 4R3I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R3I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4R3I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R3I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R3I)

(-) Exons   (0, 0)

(no "Exon" information available for 4R3I)

(-) 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:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.eeeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhh...eeeeeeee....ee.eeeee....................hhhhh..eeeeeee...ee.hhhh...hhhhh...........eehhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r3i A 344 GTSKLKYVLQDARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARSVILIFSVRESGKFQGFARLSSESHHGGSPIHWVLPAGMSAKMLGGVFKIDWICRRELPFTKSAHLTNPWNEHKPVKIGRDGQEIELECGTQLCLLFPPDESIDLYQVIHKM 507
                                   353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503    


Chain B from PDB  Type:RNA  Length:5
                                     
                 4r3i 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 4R3I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R3I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R3I)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        YTDC1_HUMAN | Q96MU7: 2yud 4r3h

(-) Related Entries Specified in the PDB File

4r3h