Modomics - A Database of RNA Modifications

ID Card:

Full name: vir like m6A methyltransferase associated
Synonym: DKFZP434I116,fSAP121
GI: 160221326
UniProt: Q69YN4
Structures: | 7VF5 | 7VF2 | 7YG4 |
Alpha Fold Predicted Structure: AF-Q69YN4-F1


PDB Structures:


7VF5

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

N 6 -methyladenosine (m 6 A) is the most abundant ribonucleotide modification among eukaryotic messenger RNAs. The m 6 A "writer" consists of the catalytic subunit m 6 A-METTL complex (MAC) and the regulatory subunit m 6 A-METTL-associated complex (MACOM), the latter being essential for enzymatic activity. Here, we report the cryo-electron microscopy (cryo-EM) structures of MACOM at a 3.0-Å resolution, uncovering that WTAP and VIRMA form the core structure of MACOM and that ZC3H13 stretches the conformation by binding VIRMA. Furthermore, the 4.4-Å resolution cryo-EM map of the MACOM-MAC complex, combined with crosslinking mass spectrometry and GST pull-down analysis, elucidates a plausible model of the m 6 A writer complex, in which MACOM binds to MAC mainly through WTAP and METTL3 interactions. In combination with in vitro RNA substrate binding and m 6 A methyltransferase activity assays, our results illustrate the molecular basis of how MACOM assembles and interacts with MAC to form an active m 6 A writer complex.

Download RCSB-PDB Structures:

Pdb Files   7VF2.pdb   7VF5.pdb   7YG4.pdb  
Pdbx/mmCIF Files   7VF2.cif   7VF5.cif   7YG4.cif  


Protein sequence:

MAVDSAMELLFLDTFKHPSAEQSSHIDVVRFPCVVYINEVRVIPPGVRAHSSLPDNRAYGETSPHTFQLDLFFNNVSKPSAPVFDRLGSLEYDENTSIIFRPNSKVNTDGLVLRGWYNCLTLAIYGSVDRVISHDRDSPPPPPPPPPPPQPQPSLKRNPKHADGEKEDQFNGSPPRPQPRGPRTPPGPPPPDDDEDDPVPLPVSGDKEEDAPHREDYFEPISPDRNSVPQEGQYSDEGEVEEEQQEEGEEDEDDVDVEEEEDEDEDDRRTVDSIPEEEEEDEEEEGEEDEEGEGDDGYEQISSDEDGIADLERETFKYPNFDVEYTAEDLASVPPMTYDPYDRELVPLLYFSCPYKTTFEIEISRMKDQGPDKENSGAIEASVKLTELLDLYREDRGAKWVTALEEIPSLIIKGLSYLQLKNTKQDSLGQLVDWTMQALNLQVALRQPIALNVRQLKAGTKLVSSLAECGAQGVTGLLQAGVISGLFELLFADHVSSSLKLNAFKALDSVISMTEGMEAFLRGRQNEKSGYQKLLELILLDQTVRVVTAGSAILQKCHFYEVLSEIKRLGDHLAEKTSSLPNHSEPDHDTDAGLERTNPEYENEVEASMDMDLLESSNISEGEIERLINLLEEVFHLMETAPHTMIQQPVKSFPTMARITGPPERDDPYPVLFRYLHSHHFLELVTLLLSIPVTSAHPGVLQATKDVLKFLAQSQKGLLFFMSEYEATNLLIRALCHFYDQDEEEGLQSDGVIDDAFALWLQDSTQTLQCITELFSHFQRCTASEETDHSDLLGTLHNLYLITFNPVGRSAVGHVFSLEKNLQSLITLMEYYSKEALGDSKSKKSVAYNYACILILVVVQSSSDVQMLEQHAASLLKLCKADENNAKLQELGKWLEPLKNLRFEINCIPNLIEYVKQNIDNLMTPEGVGLTTALRVLCNVACPPPPVEGQQKDLKWNLAVIQLFSAEGMDTFIRVLQKLNSILTQPWRLHVNMGTTLHRVTTISMARCTLTLLKTMLTELLRGGSFEFKDMRVPSALVTLHMLLCSIPLSGRLDSDEQKIQNDIIDILLTFTQGVNEKLTISEETLANNTWSLMLKEVLSSILKVPEGFFSGLILLSELLPLPLPMQTTQVIEPHDISVALNTRKLWSMHLHVQAKLLQEIVRSFSGTTCQPIQHMLRRICVQLCDLASPTALLIMRTVLDLIVEDLQSTSEDKEKQYTSQTTRLLALLDALASHKACKLAILHLINGTIKGDERYAEIFQDLLALVRSPGDSVIRQQCVEYVTSILQSLCDQDIALILPSSSEGSISELEQLSNSLPNKELMTSICDCLLATLANSESSYNCLLTCVRTMMFLAEHDYGLFHLKSSLRKNSSALHSLLKRVVSTFSKDTGELASSFLEFMRQILNSDTIGCCGDDNGLMEVEGAHTSRTMSINAAELKQLLQSKEESPENLFLELEKLVLEHSKDDDNLDSLLDSVVGLKQMLESSGDPLPLSDQDVEPVLSAPESLQNLFNNRTAYVLADVMDDQLKSMWFTPFQAEEIDTDLDLVKVDLIELSEKCCSDFDLHSELERSFLSEPSSPGRTKTTKGFKLGKHKHETFITSSGKSEYIEPAKRAHVVPPPRGRGRGGFGQGIRPHDIFRQRKQNTSRPPSMHVDDFVAAESKEVVPQDGIPPPKRPLKVSQKISSRGGFSGNRGGRGAFHSQNRFFTPPASKGNYSRREGTRGSSWSAQNTPRGNYNESRGGQSNFNRGPLPPLRPLSSTGYRPSPRDRASRGRGGLGPSWASANSGSGGSRGKFVSGGSGRGRHVRSFTR

Comments:

None





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q69YN4-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q69YN4-F1.cif  
DSSP Secondary Structures   Q69YN4.dssp  





Diseases connected to this enzyme:

Description Reaction Disease Name
Increased m6A methylation (by VIRMA) of ID2 mRNA reduced ID2 expression and promoted cell migration and invasion in HCC A:m6A
Hepatocellular carcinoma
VIRMA is upregulated in HCC. VIRMA induced m6A methylation on the 3′ UTR of GATA3 pre-mRNA, leading to the separation of the RNA-binding protein HuR and the degradation of GATA3 pre-mRNA, leading to altered GATA3 expression and thereby facilitating the malignant phenotypes of hepatoma cells. A:m6A
Hepatocellular carcinoma
m6A-related targets were altered at protein level; overexpression of the enzymes was associated with poor prognosis on overal survival; YTHDF3 is considered independent prognosis factor for OS and relapse free survival. A:m6A
Breast cancer

Publications:

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