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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ACTIVE POLYCOMB REPRESSIVE COMPLEX 2 IN THE STIMULATED STATE
 
Authors :  L. Jiao, X. Liu
Date :  20 Jun 16  (Deposition) - 19 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym./Biol. Unit :  A,B,D
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
    Chains: A
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE S288C
    Expression System Taxid: 559292
    Gene: CTHT_0029920
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
 
Molecule 2 - PUTATIVE UNCHARACTERIZED PROTEIN,ZINC FINGER DOMAIN- CONTAINING PROTEIN
    Chains: B
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE S288C
    Expression System Taxid: 559292
    Gene: CTHT_0053230, CTHT_0006210
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719), CHAETOMIUM THERMOPHILUM
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
 
Molecule 3 - PEPTIDE H3K27ME3
    Chains: D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3ZN8Ligand/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
9AC9SOFTWARELEU B:804 , CYS 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 , PHE B:922 , LEU B:925 , LYS B:927 , ARG B:2536 , HOH B:8110 , HOH B:8163 , HOH B:8256binding site for residue SAH B 8009

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro B:406 -Glu B:407
2Pro B:414 -Gln B:415
3Cys B:763 -Gly B:764

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KJH)

(-) 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:481
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee............eeeeee..........eeeeee..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
                5kjh A    6 SAEWELPRLRTSFIFQDDYKYLQDLAEFFDVKFYPYSPPGAPPVFAATSKKHAVICRLTQTTDKDANPCEIIQLIRDDGNEANCASCWSKDPITDQPLLCIAGNEGNVKVYNVTEGKLYRTLVGHGGGINDLATSPANPYIIASASDDTTIRIWSLAPEHEKQPCVCILGGEGHSYDLLSVAFHDNGRYVLSAGHDQVINLWALPEFPNEHMEIPIVIYYPHFSSSEIHNNLVDCVAFYGDLILSRACHEDTIVLWRIEGFSSDDPIPGPLDAPTPTDMTKQTRSYFTPTVSPQSRPAMFTRLAQFHTPDCGVQFFMRFRMYHVPGKHPILAFANAKSKTFFWDLARFGEYARFMADLKEAQQSYNGRVVVVDQGISLAQAQQVHGPGVGVVMKPAWLVPKVSASPDPDSPFGFSRETLQAWADMYDLSNPVGLIKAHRSLAIDGAFVGRQVGWSPEGEWCVVVGNGNRALIYQRWGKERG  557
                                    15        25 ||     42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382    || 394       404       414||     486       496       506       516       526       536       546       556 
                                                27|                                                                                                                                                                                                                                                                                                                                                             387|                      415|                                                                               
                                                 35                                                                                                                                                                                                                                                                                                                                                              390                       478                                                                               


Chain B from PDB  Type:PROTEIN  Length:807
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................ee..........eeeeeeeeee....ee....eeeeee.eee..............ee....ee..................hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhh.....hhhhhhh....hhhhh.hhhhhhhhhhhhhhhhh............ee.....ee..hhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh.............ee....ee..hhhhhh...hhhhh.................hhhhhh...............................ee........hhhhhh............hhhhhhhhhhh.hhhhhh.ee..hhhhhh....eeeee.......eeeee........eeeee..eeeehhhhhhhhhhh.........eeeee....eeee...eehhhhhhee.....eeeeeeee..eeeeeeee..........ee.................................ee....................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kjh B  197 WTVDKIASALSVLAEEVPQNHSRLVNFLLEETEKRAPQPRHLSKTDPFAHMKSKAIDANRPRPEGVPTMDVKFKQHSGEYGKSRNSGRRFQYPVVCIKPDREPVPPYRFHHAEIRKNILALNSQLNFVPHLRDVDPNSAEEQKYSAWLMDLENLDSKSGFPRSQKIAKRAQAEYAATLAPYLEPWLRKLNIECTKSNLIRFMASQPETPQQKSNLLDTYSDDAVRNASMFTEAWDRVFNDQRRVALRDILMLDKNVEPIFEALMQKVIDALGSYTTLGCLICFSHDCEHGEIERDNQKRCFSLEEIGGLMPSLRRKWAAQIEQPPCRNECYIHGTPPWSENEVGTLEWMFATIGYSLRPECFVGAILRPCWDVHRKLQELDLRLPIPKQKSLPWYDRRKKQLMSDWADATITHEHAVRELFAPCHHDGPCTAANGCPCASAGTHPVLCERFCLCTAEECPLKFTGCACHSSGKTCLQRQGRPCICVQLNRECDPTLCKGCGARERADPENAYDEVLHSTGCQNVALQRGAAKAVVLGKSQLEACGYGLFAAEDIEEGEFVIEYTGELISHDEGVRREHRRGDVFDKVSYLFTLLEQEGIWVDAAIYGNLSRYINHATDGNIMPKIMYVNHEWRIKFTAIKDIKAGEELFFNYGDNFPNLTKKLEVMLPGRGVPPLLVPKTTQPLFDPLSKVQLLPGQPLPQHPIDDSWLLLKHRDNLQDFIDLRPEEKEFLQEWDAFILRRHISSEQYLPRYFLRFVREKADWLVSKRSRGEEFSKLVATLLARRVLPERVVIEATQVLNDARGRLR 2683
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356|      369       379       389 ||    400      |415       425 ||    440       450||     463       473|      499       509       519       529       539       549  ||   574||  || 592       602     ||614      |625       635    || 651       661       671       681       691       701       711       721       731       743       753       763       773       783       793       803       813       823       833       843    || 856       866       876       886       896       906       916       926  ||  2536  ||  2556      2566      2576      2586      2596      2606      2616      2626      2636      2646      2656      2666      2676       
                                                                                                                                                                                         356|                            391|           407|           427|               451|               473|                                                           552|    575|  ||                 608|       621|              640|                                                                                          740|                                                                                                      848|                                                                          929|     2539|                                                                                                                                     
                                                                                                                                                                                          360                             393            413            433                455                490                                                            568     577  ||                  611        623               647                                                                                           743                                                                                                       852                                                                          2530      2550                                                                                                                                     
                                                                                                                                                                                                                                                                                                                                                                        580|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                         588                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain D 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
                5kjh D   23 KAARkSAP   30
                                |   
                               27-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 5KJH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Cys B:763 - Gly B:764   [ RasMol ]  
    Pro B:406 - Glu B:407   [ RasMol ]  
    Pro B:414 - Gln B:415   [ RasMol ]  
 

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  5kjh
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 Related Entries

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

UniProtKB/Swiss-Prot
        G0RYC6_CHATD | G0RYC6: 5bjs 5tqr 5vk3
        G0S8H7_CHATD | G0S8H7: 5bjs 5tqr 5vk3
        G0SDW4_CHATD | G0SDW4: 5bjs 5tqr 5vk3
        H31_HUMAN | P68431: 1cs9 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 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
UniProtKB/TrEMBL
        G0RYC6_CHATD | G0RYC6: 5kji 5kkl 5m5g
        G0S8H7_CHATD | G0S8H7: 5kji 5kkl 5m5g
        G0SDW4_CHATD | G0SDW4: 5kji 5kkl 5m5g

(-) Related Entries Specified in the PDB File

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