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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ACTIVE POLYCOMB REPRESSIVE COMPLEX 2 IN THE BASAL STATE
 
Authors :  L. Jiao, X. Liu
Date :  20 Jun 16  (Deposition) - 19 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complex, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Jiao, X. Liu
Response To Comment On "Structural Basis Of Histone H3K27 Trimethylation By An Active Polycomb Repressive Complex 2".
Science V. 354 1543 2016
PubMed-ID: 28008038  |  Reference-DOI: 10.1126/SCIENCE.AAJ2335

(-) Compounds

Molecule 1 - PUTATIVE POLYCOMB PROTEIN EED
    ChainsA
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE S288C
    Expression System Taxid559292
    GeneCTHT_0029920
    Organism ScientificCHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid759272
    StrainDSM 1495 / CBS 144.50 / IMI 039719
 
Molecule 2 - PUTATIVE UNCHARACTERIZED PROTEIN,ZINC FINGER DOMAIN- CONTAINING PROTEIN
    ChainsB
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE S288C
    Expression System Taxid559292
    GeneCTHT_0053230, CTHT_0006210
    Organism ScientificCHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719), CHAETOMIUM THERMOPHILUM
    Organism Taxid759272
    StrainDSM 1495 / CBS 144.50 / IMI 039719

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2ZN8Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:727 , CYS B:748 , CYS B:755 , CYS B:760binding site for residue ZN B 8001
2AC2SOFTWARECYS B:736 , CYS B:755 , CYS B:763 , CYS B:784binding site for residue ZN B 8002
3AC3SOFTWARECYS B:727 , CYS B:729 , CYS B:736 , CYS B:746binding site for residue ZN B 8003
4AC4SOFTWARECYS B:685 , HIS B:687 , CYS B:691 , CYS B:697binding site for residue ZN B 8004
5AC5SOFTWARECYS B:691 , CYS B:709 , CYS B:715 , CYS B:720binding site for residue ZN B 8005
6AC6SOFTWARECYS B:685 , CYS B:699 , CYS B:709 , CYS B:713binding site for residue ZN B 8006
7AC7SOFTWARECYS B:508 , CYS B:511 , CYS B:516 , HIS B:518binding site for residue ZN B 8007
8AC8SOFTWARECYS B:570 , CYS B:574 , CYS B:615 , CYS B:625binding site for residue ZN B 8008
9AC9SOFTWARECYS B:807 , GLY B:808 , TYR B:809 , LYS B:852 , VAL B:853 , SER B:854 , TYR B:855 , ARG B:877 , TYR B:878 , ASN B:880 , HIS B:881 , TYR B:918 , LEU B:925 , LYS B:927 , ARG B:2536 , HOH B:8109binding site for residue SAH B 8009

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Asp A:520 -Gly A:521
2Gly B:277 -Lys B:278
3Ala B:433 -Val B:434
4Leu B:454 -Arg B:455
5Leu B:737 -Gln B:738
6Cys B:763 -Gly B:764
7Cys B:784 -Gln B:785
8Gly B:792 -Ala B:793

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KJI)

(-) 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:479
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee..........eeee..........eeeee...eeeeeee..........eeeeeeeee.....eeeeeeee......eeeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee.hhhhh...eeeee........eeeeee.....eeeeee....eeeee............eee....eee.......eeeeeee..eeeeee....eeeeeee..........hhhhh.........eee..............eeeeeeee............eee.......eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeee.....................hhhhhhhhhhhhh...........eeee......eeeeee.....eeeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kji A    6 SAEWELPRLRTSFIFQDDYKLAEFFDVKFYPYSPPGAPPVFAATSKKHAVICRLTQTTDKDANPCEIIQLIRDDGNEANCASCWSKDPITDQPLLCIAGNEGNVKVYNVTEGKLYRTLVGHGGGINDLATSPANPYIIASASDDTTIRIWSLAPEHEKQPCVCILGGEGHSYDLLSVAFHDNGRYVLSAGHDQVINLWALPEFPNEHMEIPIVIYYPHFSSSEIHNNLVDCVAFYGDLILSRACHEDTIVLWRIEGFSSDDPIPGPLDAPTPTDMTKQTRSYFTPTVSPQSRPAMFTRLAQFHTPDCGVQFFMRFRMYHVPGKHPILAFANAKSKTFFWDLARFGEYARFMADLKEAQQSYNGRVVVVDQGQISLAQAQQVHGPGVGVVMKPAWLVPKMVSASPDPDSPFGFSRETLQAWADMYDLSNPVGLIKAHRSLAIDGAFVGRQVGWSPEGEWCVVVGNGNRALIYQRWGKERG  557
                                    15        25|       46        56        66        76        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 ||    397       407       478       488       498       508       518       528       538       548         
                                              25|                                                                                                                                                                                                                                                                                                                                                            388|                      415|                                                                                
                                               37                                                                                                                                                                                                                                                                                                                                                             390                       477                                                                                

Chain B from PDB  Type:PROTEIN  Length:761
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................eeeeeeee............eeeeee.eee..............ee....ee.....hhhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhh..........hhhhhhhhhhhhhhhhh............ee.....ee..hhhhh.hhhhhhhhhhhhhhhh.......hhhhhh.........hhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhh.............ee....ee..hhhhh....hhhhh............hhhhhhhhhhh..........................................hhhhhh............hhhhhhhhhhh.hhhhhh.....hhhhhh....eeeee.......eeeee........eeeee..eeeehhhhhhhhhh....eeeee....eeee...eehhhhhhee.....eeeeeee....eeeeeee..........ee..........................ee......ee............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kji B  196 EWTVDKIASALSVLAEEVPQNHSRLVNFLLEETEKRAPQPRHLSKTDPFAHMKSKAIDPTMDVKFKQHSGEYGKSRNSGRRFQYPVVCIKPDREPVPPYRFHHAEIRKNILALNSRSQKIAKRAQAEYAATLAPYLEPWLRKLNIEGCTKSNLIRFMASSMTPQQKSNLLDTYSDDMAVRNASMFTEAWDRVFNDQSLRRVALRDILMLDKNVEPIFEALMQKVIDALGSYTTLGCLICFSHDCEHGEIERDNQKRCFSLEEIGGLMPSLRRKWAAQIEQRPPCRNECYRIHGTGNQQVPPWSENEVGTLEWMFATIGYSQLRPECFVGAILGRPCWDVHRKLQELDLRLPIPKQKSLPWYDRRKKQLMSDWADATITHEHAVRELFAPCHHDGPCTAANGCPCASAGTHPVLCERFCLCTAEECPLKFTGCACHSSGKTCLQQREGRPCICVQLNRECDPTLCKGCGARERADPENAYDEVLHSTGCQNVALQRGAAKAVVLGKSQLEACGYGLFAAEDIEEGEFVIEYTGELISHDEGVRREHRKVSYLFTLLEQEGIWVDAAIYGNLSRYINHATDGNIMPKIMYVNHEWRIKFTAIKDIKAGEELFFNYGDNLTKKMLPGRGVPLLVPKTTQPLFDPLSKVQLLPGQPLPQHPIDDSWLLLKHRDNLQDFIDLRPEEKEFLQEWDAFILRRHISSEQYLPRYFLRFVREKADWLVSKRSRGEEFSKLVATLLARRVLPERVVIEATQVLNDARGRLR 2683
                                   205       215       225       235       245       264       274       284       294       304       314    || 365       375       385       395       411       421      |435       445      |456       466      |492       502       512       522       532       542       552||     576    || 588       598       608||     619       629       639||     655       665       675       685       695       705       715       725       735  ||   746       756       766       776       786       796       806       816       826       836     ||855       865       875       885       895       905       915     ||928|     2552      2562      2572      2582      2592      2602      2612      2622      2632      2642      2652      2662      2672      2682 
                                                                                   253|                                                     319|                                        404|              428|                452|                473|                                                            553|          581|                      609|                          640|                                                                                        738|                                                                                                   842|                                                                  921|  ||  2538|                                                                                                                                     
                                                                                    263                                                      361                                         411               433                 454                 490                                                             568           584                       611                           647                                                                                         740                                                                                                    852                                                                   925  ||   2550                                                                                                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     928|                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     2532                                                                                                                                            

   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 5KJI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:433 - Val B:434   [ RasMol ]  
    Asp A:520 - Gly A:521   [ RasMol ]  
    Cys B:763 - Gly B:764   [ RasMol ]  
    Cys B:784 - Gln B:785   [ RasMol ]  
    Gly B:277 - Lys B:278   [ RasMol ]  
    Gly B:792 - Ala B:793   [ RasMol ]  
    Leu B:454 - Arg B:455   [ RasMol ]  
    Leu B:737 - Gln B:738   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        G0RYC6_CHATD | G0RYC65bjs 5tqr 5vk3
        G0S8H7_CHATD | G0S8H75bjs 5tqr 5vk3
        G0SDW4_CHATD | G0SDW45bjs 5tqr 5vk3
        H31_HUMAN | P684311cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
UniProtKB/TrEMBL
        G0RYC6_CHATD | G0RYC65kjh 5kkl 5m5g
        G0S8H7_CHATD | G0S8H75kjh 5kkl 5m5g
        G0SDW4_CHATD | G0SDW45kjh 5kkl 5m5g

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5KJI)