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(-) Description

Title :  CRYSTAL STRUCTURE OF ATXR5 SET DOMAIN IN COMPLEX WITH HISTONE H3 DI-METHYLATED ON R26
 
Authors :  E. Bergamin, S. Sarvan, J. Malette, M. Eram, S. Yeung, V. Mongeon, M. Jos J. S. Brunzelle, S. D. Michaels, A. Blais, M. Vedadi, J. -F. Couture
Date :  26 Mar 17  (Deposition) - 05 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Histone, Nucleosome, Methyltransferases, Transferase-Dna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Bergamin, S. Sarvan, J. Malette, M. S. Eram, S. Yeung, V. Mongeon, M. Joshi, J. S. Brunzelle, S. D. Michaels, A. Blais, M. Vedadi, J. F. Couture
Molecular Basis For The Methylation Specificity Of Atxr5 Fo Histone H3.
Nucleic Acids Res. 2017
PubMed-ID: 28383693  |  Reference-DOI: 10.1093/NAR/GKX224

(-) Compounds

Molecule 1 - PROBABLE HISTONE-LYSINE N-METHYLTRANSFERASE ATXR5
    Chains: A, B
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 146-374
    Gene: ATXR5, RCOM_1460410
    Organism Common: CASTOR BEAN
    Organism Scientific: RICINUS COMMUNIS
    Organism Taxid: 3988
 
Molecule 2 - HISTONE H3.2
    Chains: C, D
    Engineered: YES
    Fragment: RESIDUES 22-36
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: HISTONE H3.1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1DA22Mod. Amino AcidNG,NG-DIMETHYL-L-ARGININE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DA21Mod. Amino AcidNG,NG-DIMETHYL-L-ARGININE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1DA21Mod. Amino AcidNG,NG-DIMETHYL-L-ARGININE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:187 , ARG A:249 , GLU A:250 , PHE A:252 , ASP A:285 , ARG A:312 , PHE A:313 , SER A:315 , GLY A:316 , TYR A:361 , TYR A:368 , PHE A:373 , VAL A:374 , HOH A:514 , HOH A:540binding site for residue SAH A 401
2AC2SOFTWAREARG B:249 , GLU B:250 , GLY B:251 , PHE B:252 , ASP B:285 , SER B:286 , ARG B:312 , PHE B:313 , SER B:315 , GLY B:316 , TYR B:361 , TYR B:368 , PHE B:373 , VAL B:374 , HOH B:507 , LYS D:27binding site for residue SAH B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5VAH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5VAH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5VAH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VAH)

(-) Exons   (0, 0)

(no "Exon" information available for 5VAH)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhh..ee...ee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....eeeeee...eeeeee........eeee..eeeee.hhh........eeee........eeee...eehhhhhhee......hhhhhh.eeeeeeee..eeeeeeee..........ee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vah A 160 RLLPFVSSEDPAQRLKQMGTLASALTELQMEFSDDLTYGMAPRSANQARFEEGGMQVLTKEDIETLEQCRAMCKRGDCPPLLVVFDSREGFTVEADGQIKDMTFIAEYTGDVDYIRNREHDDCDSMMTLLLAKDPSSSLVICPDKRGNIARFISGINNHTLDAKKKQNCKCVRYSVNGECRVFLVATRDIAKGERLYYDYNGYEHEYPTQHFV 374
                                   169       179       189       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371   
                                                               197|                                                                                                                                                                              
                                                                200                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh..ee...ee.........hhhhh.......hhhhhhhhhhhhhhhhhh....eeeeee...eeeeee........eeee..eeeee.hhh.......eeeee...hhhh.eeee...eehhhhhhee......hhhhhh.eeeeeeee..eeeeeeee..........ee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vah B 159 RRLLPFVSSEDPAQRLKQMGTLASALTELQMEFSDDLTYGMAPRSANQARFEEGGMQVLTKEDIETLEQCRAMCKRGDCPPLLVVFDSREGFTVEADGQIKDMTFIAEYTGDVDYIRNREHDDCDSMMTLLLAKDPSSSLVICPDKRGNIARFISGINNHTLDAKKKQNCKCVRYSVNGECRVFLVATRDIAKGERLYYDYNGYEHEYPTQHFV 374
                                   168       178       188       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370    
                                                                197|                                                                                                                                                                              
                                                                 200                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5vah C  23 KAArKSAPATGGV  35
                               |    32   
                              26-DA2     


Chain D from PDB  Type:PROTEIN  Length:15
                                               
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .....ee........ Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 5vah D  21 ATKAArKSAPATGGV  35
                                 |  30     
                                26-DA2
   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 5VAH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VAH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VAH)

(-) Gene Ontology  (15, 16)

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  5vah
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  ATXR5_RICCO | B9RU15
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  H32_ARATH | P59226
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  2.1.1.43
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 Related Entries

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

UniProtKB/Swiss-Prot
        ATXR5_RICCO | B9RU15: 4o30 5va6 5vac 5vbc
        H32_ARATH | P59226: 4ft2 4ft4 4iur 4iut 4iuu 4iuv 5hh7 5vbc

(-) Related Entries Specified in the PDB File

5vab 5vac