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(-) Description

Title :  STRUCTURE OF G9A SET-DOMAIN WITH H3K9M MUTANT PEPTIDE AND SAM
 
Authors :  K. Xu, L. Tong
Date :  16 Aug 16  (Deposition) - 05 Oct 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,P,Q
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B,Q  (1x)
Keywords :  Histone Methyltransferase, Set Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Shan, J. Wang, K. Xu, H. Chen, J. X. Yue, S. Andrews, J. J. Moresco, J. R. Yates, P. L. Nagy, L. Tong, S. Jia
A Histone H3K9M Mutation Traps Histone Methyltransferase Clr4 To Prevent Heterochromatin Spreading.
Elife V. 5 2016
PubMed-ID: 27648579  |  Reference-DOI: 10.7554/ELIFE.17903

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE EHMT2
    Chains: A, B
    EC Number: 2.1.1.-, 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: EHMT2, BAT8, C6ORF30, G9A, KMT1C, NG36
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EUCHROMATIC HISTONE-LYSINE N-METHYLTRANSFERASE 2,HLA-B- ASSOCIATED TRANSCRIPT 8,HISTONE H3-K9 METHYLTRANSFERASE 3,H3-K9- HMTASE 3,LYSINE N-METHYLTRANSFERASE 1C,PROTEIN G9A
 
Molecule 2 - H3K9 MUTANT PEPTIDE
    Chains: P, Q
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABPQ
Biological Unit 1 (1x): A P 
Biological Unit 2 (1x):  B Q

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
2ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:974 , CYS A:987 , CYS A:1017 , CYS A:1021binding site for residue ZN A 1300
02AC2SOFTWARECYS A:980 , CYS A:1017 , CYS A:1023 , CYS A:1027binding site for residue ZN A 1301
03AC3SOFTWARECYS A:974 , CYS A:976 , CYS A:980 , CYS A:985binding site for residue ZN A 1302
04AC4SOFTWARECYS A:1115 , CYS A:1168 , CYS A:1170 , CYS A:1175binding site for residue ZN A 1303
05AC5SOFTWAREMET A:1048 , TRP A:1050 , SER A:1084 , TYR A:1085 , ARG A:1109 , PHE A:1110 , ILE A:1111 , ASN A:1112 , HIS A:1113 , TYR A:1154 , PHE A:1158 , PHE A:1166 , THR A:1167 , CYS A:1168 , GLN A:1169 , HOH A:1454 , HOH A:1483 , HOH A:1486 , HOH A:1593 , HOH A:1595binding site for residue SAM A 1304
06AC6SOFTWARECYS B:974 , CYS B:976 , CYS B:980 , CYS B:985binding site for residue ZN B 1300
07AC7SOFTWARECYS B:974 , CYS B:987 , CYS B:1017 , CYS B:1021binding site for residue ZN B 1301
08AC8SOFTWARECYS B:980 , CYS B:1017 , CYS B:1023 , CYS B:1027binding site for residue ZN B 1302
09AC9SOFTWARECYS B:1115 , CYS B:1168 , CYS B:1170 , CYS B:1175binding site for residue ZN B 1303
10AD1SOFTWAREMET B:1048 , TRP B:1050 , SER B:1084 , TYR B:1085 , ARG B:1109 , PHE B:1110 , ILE B:1111 , ASN B:1112 , HIS B:1113 , TYR B:1154 , PHE B:1158 , PHE B:1166 , THR B:1167 , CYS B:1168 , GLN B:1169 , HOH B:1419 , HOH B:1472 , HOH B:1534 , HOH B:1556 , HOH B:1583 , HOH B:1609binding site for residue SAM B 1304

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:937 -A:946
2B:937 -B:946

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5T0K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T0K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T0K)

(-) Exons   (0, 0)

(no "Exon" information available for 5T0K)

(-) 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:264
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................ee............ee....ee........hhhhh.............hhhhhhh......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhh.......eee....eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh..............hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5t0k A  920 KIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQS 1187
                                   929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089||    1103      1113      1123      1133      1143      1153      1163      1173      1183    
                                                                                                                                                                                                   1090|                                                                                            
                                                                                                                                                                                                    1095                                                                                            


Chain B from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...........ee............ee....ee........hhhhh.............hhhhhhh...............ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhh.......eee........eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh..............hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5t0k B  921 IICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDNKDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQSRLARL 1192
                                   930       940       950       960       970       980       990      1000  ||  1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187     
                                                                                                           1003|                                                                                                                                                                                     
                                                                                                            1011                                                                                                                                                                                     


Chain P from PDB  Type:PROTEIN  Length:10
                                           
               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
                5t0k P    3 TKQTARMSTG   12
                                    12


Chain Q from PDB  Type:PROTEIN  Length:10
                                           
               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
                5t0k Q    3 TKQTARMSTG   12
                                    12
   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 5T0K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T0K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T0K)

(-) Gene Ontology  (51, 55)

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  5t0k
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  H31_HUMAN | P68431
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 Related Entries

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

UniProtKB/Swiss-Prot
        EHMT2_HUMAN | Q96KQ7: 2o8j 3dm1 3k5k 3rjw 4nvq 5jhn 5jin 5jiy 5jj0 5t0m 5ttf 5tuy 5vsc
        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 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6

(-) Related Entries Specified in the PDB File

5t0m