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(-) Description

Title :  STRUCTURE OF YTH-YTHDF2 IN THE FREE STATE
 
Authors :  F. D. Li, D. B. Zhao, J. H. Wu, Y. Y. Shi
Date :  19 Sep 14  (Deposition) - 24 Dec 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Rna Binding, Atypical Beta-Propeller, M6A Methylated Rna, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Li, D. Zhao, J. Wu, Y. Shi
Structure Of The Yth Domain Of Human Ythdf2 In Complex With An M(6)A Mononucleotide Reveals An Aromatic Cage For M(6)A Recognition.
Cell Res. V. 24 1490 2014
PubMed-ID: 25412658  |  Reference-DOI: 10.1038/CR.2014.153

(-) Compounds

Molecule 1 - YTH DOMAIN-CONTAINING FAMILY PROTEIN 2
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 408-552
    Gene: YTHDF2, HGRG8
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CLL-ASSOCIATED ANTIGEN KW-14, HIGH-GLUCOSE-REGULATED PROTEIN 8, RENAL CARCINOMA ANTIGEN NY-REN-2

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:416 , VAL A:461 , GLY A:463 , SER A:464 , GLY A:465 , ASN A:507 , HOH A:715 , HOH A:779BINDING SITE FOR RESIDUE SO4 A 601
2AC2SOFTWARELYS B:416 , VAL B:461 , ASN B:462 , GLY B:463 , SER B:464 , GLY B:465 , ASN B:507 , THR B:524 , HOH B:725 , HOH B:756 , HOH B:759 , HOH B:777BINDING SITE FOR RESIDUE SO4 B 601
3AC3SOFTWARELYS C:416 , SER C:460 , GLY C:463 , SER C:464 , GLY C:465 , ASN C:507 , THR C:524 , HOH C:729BINDING SITE FOR RESIDUE SO4 C 601
4AC4SOFTWARELYS D:416 , VAL D:461 , GLY D:463 , SER D:464 , GLY D:465 , ASN D:507 , THR D:524 , HOH D:755 , HOH D:758 , HOH D:764BINDING SITE FOR RESIDUE SO4 D 601
5AC5SOFTWARELYS E:416 , SER E:460 , VAL E:461 , GLY E:463 , SER E:464 , GLY E:465 , ASN E:507 , HOH E:756BINDING SITE FOR RESIDUE SO4 E 601
6AC6SOFTWARELYS F:416 , SER F:460 , ASN F:462 , GLY F:463 , SER F:464 , GLY F:465 , ASN F:507BINDING SITE FOR RESIDUE SO4 F 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RDO)

(-) Sequences/Alignments

Asymmetric 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:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhhhh....eeeeeee....eeeeeeee.....................eeeeeeeeeeee.hhh....hhhhh..hhhhh....eehhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rdo A 400 ENLYFQHMKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYK 548
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539         


Chain B from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               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
                 4rdo B 403 YFQHMKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYK 548
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542      


Chain C from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               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
                 4rdo C 400 ENLYFQHMKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASY 547
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539        


Chain D from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhhhh....eeeeeee....eeeeeeee.....................eeeeeeeeeeee.hhh....hhhhh..hhhhh....eehhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rdo D 402 LYFQHMKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASY 547
                                   411       421       431       441       451       461       471       481       491       501       511       521       531       541      


Chain E from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhhhh....eeeeeee....eeeeeeee.....................eeeeeeeeeeee.hhh....hhhhh..hhhhh....eehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rdo E 407 MKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASY 547
                                   416       426       436       446       456       466       476       486       496       506       516       526       536       546 


Chain F from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhhhhhee..hhhhhhhhhhhhhhh.....eeeeeee....eeeeeeee.....................eeeeeeeeeeee.hhh...........hhhhh....eehhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rdo F 409 HGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYK 548
                                   418       428       438       448       458       468       478       488       498       508       518       528       538       548
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4RDO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        YTHD2_HUMAN | Q9Y5A9: 4rdn 4wqn

(-) Related Entries Specified in the PDB File

4rdn