Modomics - A Database of RNA Modifications

ID Card:

Full name: YTH N6-methyladenosine RNA binding protein 1
Synonym: FLJ20391
GI: 28380041
UniProt: Q9BYJ9
Structures: | 4RCI | 4RCJ |
Alpha Fold Predicted Structure: AF-Q9BYJ9-F1


PDB Structures:


4RCI

Structure Description:

Title: Crystal structure of YTHDF1 YTH domain
Classification: RNA BINDING PROTEIN
Technique: X-Ray Diffraction
Resolution: 1.97
R value free: 0.229
R value observed: 0.19
R value work: 0.189

Abstract of the PDB Structure's related Publication:

N(6)-Methyladenosine (m(6)A) is the most abundant internal modification in RNA and is specifically recognized by YT521-B homology (YTH) domain-containing proteins. Recently we reported that YTHDC1 prefers guanosine and disfavors adenosine at the position preceding the m(6)A nucleotide in RNA and preferentially binds to the GG(m(6)A)C sequence. Now we systematically characterized the binding affinities of the YTH domains of three other human proteins and yeast YTH domain protein Pho92 and determined the crystal structures of the YTH domains of human YTHDF1 and yeast Pho92 in complex with a 5-mer m(6)A RNA, respectively. Our binding and structural data revealed that the YTH domain used a conserved aromatic cage to recognize m(6)A. Nevertheless, none of these YTH domains, except YTHDC1, display sequence selectivity at the position preceding the m(6)A modification. Structural comparison of these different YTH domains revealed that among those, only YTHDC1 harbors a distinctly selective binding pocket for the nucleotide preceding the m(6)A nucleotide.

Download RCSB-PDB Structures:

Pdb Files   4RCI.pdb   4RCJ.pdb  
Pdbx/mmCIF Files   4RCI.cif   4RCJ.cif  


Protein sequence:

MSATSVDTQRTKGQDNKVQNGSLHQKDTVHDNDFEPYLTGQSNQSNSYPSMSDPYLSSYYPPSIGFPYSLNEAPWSTAGDPPIPYLTTYGQLSNGDHHFMHDAVFGQPGGLGNNIYQHRFNFFPENPAFSAWGTSGSQGQQTQSSAYGSSYTYPPSSLGGTVVDGQPGFHSDTLSKAPGMNSLEQGMVGLKIGDVSSSAVKTVGSVVSSVALTGVLSGNGGTNVNMPVSKPTSWAAIASKPAKPQPKMKTKSGPVMGGGLPPPPIKHNMDIGTWDNKGPVPKAPVPQQAPSPQAAPQPQQVAQPLPAQPPALAQPQYQSPQQPPQTRWVAPRNRNAAFGQSGGAGSDSNSPGNVQPNSAPSVESHPVLEKLKAAHSYNPKEFEWNLKSGRVFIIKSYSEDDIHRSIKYSIWCSTEHGNKRLDSAFRCMSSKGPVYLLFSVNGSGHFCGVAEMKSPVDYGTSAGVWSQDKWKGKFDVQWIFVKDVPNNQLRHIRLENNDNKPVTNSRDTQEVPLEKAKQVLKIISSYKHTTSIFDDFAHYEKRQEEEEVVRKERQSRNKQ

Comments:





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M S A T S V D T Q R T K G Q D N K V Q N G S L H Q K D T V H D N D F E P Y L T G Q S N Q S N S Y P S M S D P Y L S S Y Y P P S I G F P Y S L N E A P W S T A G D P P I P Y L T T Y G Q L S N G D H H F M H D A V F G Q P G G L G N N I Y Q H R F N F F P E N P A F S A W G T S G S Q G Q Q T Q S S A Y G S S Y T Y P P S S L G G T V V D G Q P G F H S D T L S K A P G M N S L E Q G M V G L K I G D V S S S A V K T V G S V V S S V A L T G V L S G N G G T N V N M P V S K P T S W A A I A S K P A K P Q P K M K T K S G P V M G G G L P P P P I K H N M D I G T W D N K G P V P K A P V P Q Q A P S P Q A A P Q P Q Q V A Q P L P A Q P P A L A Q P Q Y Q S P Q Q P P Q T R W V A P R N R N A A F G Q S G G A G S D S N S P G N V Q P N S A P S V E S H P V L E K L K A A H S Y N P K E F E W N L K S G R V F I I K S Y S E D D I H R S I K Y S I W C S T E H G N K R L D S A F R C M S S K G P V Y L L F S V N G S G H F C G V A E M K S P V D Y G T S A G V W S Q D K W K G K F D V Q W I F V K D V P N N Q L R H I R L E N N D N K P V T N S R D T Q E V P L E K A K Q V L K I I S S Y K H T T S I F D D F A H Y E K R Q E E E E V V R K E R Q S R N K Q
50100150200250300350400450500550SequenceGHTBSN

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-Q9BYJ9-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9BYJ9-F1.cif  
DSSP Secondary Structures   Q9BYJ9.dssp  





Diseases connected to this enzyme:

Publications: