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(-) Description

Title :  CRYSTAL STRUCTURE OF N6-METHYLADENOSINE RNA READER YTHDF2
 
Authors :  T. Zhu, I. A. Roundtree, P. Wang, X. Wang, L. Wang, C. Sun, Y. Tian, J. Li, C
Date :  22 Oct 14  (Deposition) - 19 Nov 14  (Release) - 10 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  N6-Methyladenosine Rna Reader, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Zhu, I. A. Roundtree, P. Wang, X. Wang, L. Wang, C. Sun, Y. Tian, J. Li, C. He, Y. Xu
Crystal Structure Of The Yth Domain Of Ythdf2 Reveals Mechanism For Recognition Of N6-Methyladenosine.
Cell Res. V. 24 1493 2014
PubMed-ID: 25412661  |  Reference-DOI: 10.1038/CR.2014.152

(-) Compounds

Molecule 1 - YTH DOMAIN-CONTAINING FAMILY PROTEIN 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 383-553
    Gene: YTHDF2, HGRG8
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: N6-METHYLADENOSINE RNA READER YTHDF2,CLL-ASSOCIATED ANTIGEN KW-14,HIGH-GLUCOSE-REGULATED PROTEIN 8,RENAL CARCINOMA ANTIGEN NY- REN-2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:425 , LYS A:428 , TYR A:429 , GLU A:516 , ASN A:520 , LYS A:536binding site for residue GOL A 601
2AC2SOFTWARELYS B:416 , ASN B:462 , GLY B:463 , SER B:464 , GLY B:465binding site for residue EDO B 601
3AC3SOFTWAREARG B:425 , LYS B:428 , TYR B:429 , ASN B:520 , LYS B:536binding site for residue EDO B 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhhhh....eeeeeee....eeeeeeee.....................eeeeeeeeeeee.hhh...........hhhhh......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wqn A 398 YNPKDFDWNLKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYK 548
                                   407       417       427       437       447       457       467       477       487       497       507       517       527       537       547 


Chain B from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhhhh....eeeeeee....eeeeeeee.....................eeeeeeeeeeee.hhh...........hhhhh....eehhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wqn B 398 YNPKDFDWNLKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYK 548
                                   407       417       427       437       447       457       467       477       487       497       507       517       527       537       547
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4WQN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (10, 10)

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        YTHD2_HUMAN | Q9Y5A9: 4rdn 4rdo

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