Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ATXR5 IN COMPLEX WITH HISTONE H3.1 AND ADOHCY
 
Authors :  E. Bergamin, V. Mongeon, J. F. Couture
Date :  17 Dec 13  (Deposition) - 26 Mar 14  (Release) - 24 Sep 14  (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 :  Histone Methylation, Chromatin, Epigenetics, Trithorax, Set Domain, Lysine Methyltransferases, Pcna, Histone H3, Nucleus, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Jacob, E. Bergamin, M. T. Donoghue, V. Mongeon, C. Leblanc, P. Voigt C. J. Underwood, J. S. Brunzelle, S. D. Michaels, D. Reinberg, J. F. Couture, R. A. Martienssen
Selective Methylation Of Histone H3 Variant H3. 1 Regulates Heterochromatin Replication.
Science V. 343 1249 2014
PubMed-ID: 24626927  |  Reference-DOI: 10.1126/SCIENCE.1248357

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE ATXR6, PUTATIVE
    ChainsA, B
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentSET DOMAIN, UNP RESIDUES 146-374
    GeneRCOM_1460410
    Organism CommonCASTOR BEAN
    Organism ScientificRICINUS COMMUNIS
    Organism Taxid3988
 
Molecule 2 - HISTONE H3.1
    ChainsC, D
    EngineeredYES
    Other DetailsSYNTHETIC PEPTIDE (GENESCRIPT), HISTONE H3
    SyntheticYES

 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  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:249 , GLU A:250 , PHE A:252 , ASP A:285 , SER A:286 , 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:505 , HOH A:520 , HOH A:600 , HOH A:615 , HOH A:648 , LYS C:27BINDING SITE FOR RESIDUE SAH A 401
2AC2SOFTWAREMET A:177BINDING SITE FOR RESIDUE DMS A 402
3AC3SOFTWARELEU B:187 , GLU B:250 , PHE B:252 , ASP B:285 , ARG B:312 , SER B:315 , GLY B:316 , TYR B:361 , TYR B:368 , PHE B:373 , VAL B:374 , HOH B:590 , LYS D:27BINDING SITE FOR RESIDUE SAH B 401
4AC4SOFTWAREGLN B:176 , MET B:177 , LEU B:180 , CYS B:239 , PRO B:240 , LEU B:242 , ILE B:310 , HOH B:568BINDING SITE FOR RESIDUE BME B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O30)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4O30)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O30)

(-) Exons   (0, 0)

(no "Exon" information available for 4O30)

(-) 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:217
                                                                                                                                                                                                                                                         
               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...hhhh.eeee...eehhhhhhee......hhhhhh.eeeeeeee..eeeeeeee..........ee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o30 A 158 RRRLLPFVSSEDPAQRLKQMGTLASALTELQMEFSDDLTYSSGMAPRSANQARFEEGGMQVLTKEDIETLEQCRAMCKRGDCPPLLVVFDSREGFTVEADGQIKDMTFIAEYTGDVDYIRNREHDDCDSMMTLLLAKDPSKSLVICPDKRGNIARFISGINNHTLDGKKKQNCKCVRYSVNGECRVFLVATRDIAKGERLYYDYNGYEHEYPTQHFV 374
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       

Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               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........eeee...eehhhhhhee......hhhhhh.eeeeeeee..eeeeeeee..........ee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4o30 B 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 C from PDB  Type:PROTEIN  Length:14
                                              
               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
                 4o30 C  23 KAARKSAPATGGVK  36
                                    32    

Chain D from PDB  Type:PROTEIN  Length:12
                                            
               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
                 4o30 D  24 AARKSAPATGGV  35
                                    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 4O30)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O30)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O30)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4o30)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4o30
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ATXR5_RICCO | B9RU15
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.43
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ATXR5_RICCO | B9RU15
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ATXR5_RICCO | B9RU155va6 5vac 5vah 5vbc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4O30)