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(-) Description

Title :  CRYSTAL STRUCTURE OF EED IN COMPLEX WITH A TRIMETHYLATED HISTONE H1K26 PEPTIDE
 
Authors :  N. Justin, M. L. Sharpe, S. Martin, W. R. Taylor, V. De Marco, S. J. Gamblin
Date :  03 Aug 09  (Deposition) - 15 Sep 09  (Release) - 20 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Wd40 Domain, Alternative Initiation, Alternative Splicing, Chromatin Regulator, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription Regulation, Wd Repeat, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Margueron, N. Justin, K. Ohno, M. L. Sharpe, J. Son, W. J. Drury, P. Voigt, S. R. Martin, W. R. Taylor, V. De Marco, V. Pirrotta, D. Reinberg, S. J. Gamblin
Role Of The Polycomb Protein Eed In The Propagation Of Repressive Histone Marks.
Nature V. 461 762 2009
PubMed-ID: 19767730  |  Reference-DOI: 10.1038/NATURE08398
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYCOMB PROTEIN EED
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentEED RESIDUES 77-441
    GeneEED
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHEED, WD PROTEIN ASSOCIATING WITH INTEGRIN CYTOPLASMIC TAILS 1, WAIT-1
 
Molecule 2 - HISTONE H1K26 PEPTIDE
    ChainsB
    EngineeredYES
    FragmentHISTONE H1K26 PEPTIDE RESIDUES 21-31
    Other DetailsSYNTHETIC PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE

(-) Sites  (0, 0)

(no "Site" information available for 3IIY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IIY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IIY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_078316R236TEED_HUMANUnclassified  ---AR236T
2UniProtVAR_078317R302SEED_HUMANUnclassified  ---AR302S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.EED_HUMAN206-220  1A:206-220

(-) Exons   (0, 0)

(no "Exon" information available for 3IIY)

(-) Sequences/Alignments

Asymmetric/Biological 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:364
 aligned with EED_HUMAN | O75530 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:364
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436    
            EED_HUMAN    77 KCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL 440
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee......eeeeee..........eeeeee..eeeeeee.....eeeeeeee.......eeeeeeee......eeeeeee...eeeee......eeeeee.....eeeeee......eeeeee....eeeee....eeeeee.........eeeeee.....eeeeee....eeeee..hhhhhhhhhhhhhhhhhhh......eee....eee.........eeeee..eeeee....eeeeeee.....hhhhh......eeeeeeee...........ee.....eeeee.....eeeee....hhhhheeeee........eeeeee.....eeeeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------T-----------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------WD_REPEATS_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iiy A  77 KCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSTDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL 440
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436    

Chain B from PDB  Type:PROTEIN  Length:8
                                        
               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
                 3iiy B  24 ARkSAGAA  31
                              |     
                             26-M3L 

   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 3IIY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IIY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IIY)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EED_HUMAN | O75530)
molecular function
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0042054    histone methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or lysine residue.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0016571    histone methylation    The modification of histones by addition of methyl groups.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0061087    positive regulation of histone H3-K27 methylation    Any process that increases the rate, frequency, or extent of histone H3-K27 methylation. Histone H3-K27 methylation is the modification of histone H3 by addition of a methyl group to lysine at position 27 of the histone.
    GO:0006349    regulation of gene expression by genetic imprinting    Heritable alterations in the activity of a gene that depend on whether it passed through the paternal or the maternal germline, but that are not encoded by DNA itself.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0021510    spinal cord development    The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0035098    ESC/E(Z) complex    A multimeric protein complex that can methylate lysine-27 and lysine-9 residues of histone H3. In Drosophila the core subunits of the complex include ESC, E(Z), CAF1 (NURF-55) and SU(Z)12. In mammals the core subunits of the complex include EED, EZH2, SUZ12 and RBBP4.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0045120    pronucleus    The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents.
    GO:0001739    sex chromatin    Chromatin that is part of a sex chromosome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EED_HUMAN | O755303iiw 3ij0 3ij1 3ijc 3jpx 3jzg 3jzh 3jzn 3k26 3k27 4x3e 5gsa 5h13 5h14 5h15 5h17 5h19 5h24 5h25 5hyn 5ij7 5ij8 5k0m 5ls6 5ttw 5u5h 5u5k 5u5t 5u62 5u69 5u6d 5u8a 5u8f 5wuk

(-) Related Entries Specified in the PDB File

2qxv STRUCTURAL BASIS OF EZH2 RECOGNITION BY EED
3iiw CRYSTAL STRUCTURE OF EED IN COMPLEX WITH A TRIMETHYLATED HISTONE H3K27 PEPTIDE
3ij0 CRYSTAL STRUCTURE OF EED IN COMPLEX WITH A TRIMETHYLATED HISTONE H3K9 PEPTIDE
3ij1 CRYSTAL STRUCTURE OF EED IN COMPLEX WITH A TRIMETHYLATED HISTONE H4K20 PEPTIDE
3ijc CRYSTAL STRUCTURE OF EED IN COMPLEX WITH NDSB-195