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(-) Description

Title :  CRYSTAL STRUCTURE OF ATXR5 IN COMPLEX WITH HISTONE H3.1
 
Authors :  J. -F. Couture, E. Bergamin
Date :  29 Mar 17  (Deposition) - 19 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Nucleosome, Methylation, 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: SET DOMAIN RESIDUES 146-374
    Gene: ATXR5, RCOM_1460410
    Organism Common: CASTOR BEAN
    Organism Scientific: RICINUS COMMUNIS
    Organism Taxid: 3988
 
Molecule 2 - HISTONE H3.1 PEPTIDE
    Chains: C, D
    Engineered: YES
    Fragment: RESIDUES 24-37
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: HISTONE H3.2
    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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1DMS-1Ligand/IonDIMETHYL SULFOXIDE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:249 , GLU A:250 , PHE A:252 , ASP A:285 , SER A:286 , ARG A:312 , SER A:315 , GLY A:316 , TYR A:361 , TYR A:368 , PHE A:373 , VAL A:374 , HOH A:513 , HOH A:539 , HOH A:552 , HOH A:559 , HOH A:565 , LYS C:27binding site for residue SAH A 401
2AC2SOFTWAREMET A:177binding site for residue DMS A 402
3AC3SOFTWAREGLU B:250 , PHE B:252 , ARG B:312 , SER B:315 , GLY B:316 , TYR B:361 , TYR B:368 , PHE B:373 , VAL B:374 , HOH B:569 , LYS D:27binding site for residue SAH B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VBC)

(-) 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:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh..ee...ee......hhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....eeeeee...eeeeee........eeee..eeeee.hhhh......eeeee...hhhh.eeee...eehhhhhhee......hhhhhh.eeeeeeee..eeeeeeee..........ee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vbc A 159 RRLLPFVSSEDPAQRLKQMGTLASALTELQMEFSDDLTYSSGMAPRSANQARFEEGGMQVLTKEDIETLEQCRAMCKRGDCPPLLVVFDSREGFTVEADGQIKDMTFIAEYTGDVDYIRNREHDDCDSMMTLLLAKDPSKSLVICPDKRGNIARFISGINNHTLDGKKKQNCKCVRYSVNGECRVFLVATRDIAKGERLYYDYNGYEHEYPTQHFV 374
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368      


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhh..ee...........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....eeeeee...eeeeee........eeee...eeee.hhhh......eeeee...hhhh.eeee...eehhhhhhee......hhhhhh.eeeeeeee..eeeeeeee..........ee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vbc B 160 RLLPFVSSEDPAQRLKQMGTLASALTELQMEFSDDLTYSSGMAPRSANQARFEEGGMQVLTKEDIETLEQCRAMCKRGDCPPLLVVFDSREGFTVEADGQIKDMTFIAEYTGDVDYIRNREHDDCDSMMTLLLAKDPSKSLVICPDKRGNIARFISGINNHTLDGKKKQNCKCVRYSVNGECRVFLVATRDIAKGERLYYDYNGYEHEYPTQHFV 374
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369     


Chain C from PDB  Type:PROTEIN  Length:14
                                              
               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
                 5vbc C  23 KAARKSAPATGGVK  36
                                    32    


Chain D from PDB  Type:PROTEIN  Length:13
                                             
               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
                 5vbc D  24 AARKSAPATGGVK  36
                                    33
   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 5VBC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 16)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5va6 5vab 5vac 5vah