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(-) Description

Title :  A HISTONE H3K9M MUTATION TRAPS HISTONE METHYLTRANSFERASE CLR4 TO PREVENT HETEROCHROMATIN SPREADING
 
Authors :  K. Xu, L. Tong
Date :  16 Aug 16  (Deposition) - 05 Oct 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,P
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B,C  (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
    Fragment: UNP RESIDUES 879-1159
    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 - THR-LYS-GLN-THR-ALA-ARG-NLE-SER-THR-GLY
    Chains: P, C
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCP
Biological Unit 1 (1x): A  P
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1NLE2Mod. Amino AcidNORLEUCINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SAM2Ligand/IonS-ADENOSYLMETHIONINE
4ZN8Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1NLE1Mod. Amino AcidNORLEUCINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SAM1Ligand/IonS-ADENOSYLMETHIONINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1NLE1Mod. Amino AcidNORLEUCINE
2SAH-1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SAM1Ligand/IonS-ADENOSYLMETHIONINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:974 , CYS A:987 , CYS A:1017 , CYS A:1021binding site for residue ZN A 1201
02AC2SOFTWARECYS A:980 , CYS A:1017 , CYS A:1023 , CYS A:1027binding site for residue ZN A 1202
03AC3SOFTWARECYS A:974 , CYS A:976 , CYS A:980 , CYS A:985binding site for residue ZN A 1203
04AC4SOFTWARECYS A:1115 , CYS A:1168 , CYS A:1170 , CYS A:1175binding site for residue ZN A 1204
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:1166 , THR A:1167 , CYS A:1168 , GLN A:1169 , SAH A:1206 , HOH A:1404 , HOH A:1422 , HOH A:1423 , HOH A:1425binding site for residue SAM A 1205
06AC6SOFTWAREMET 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:1166 , THR A:1167 , CYS A:1168 , GLN A:1169 , SAM A:1205 , HOH A:1404 , HOH A:1422 , HOH A:1423 , HOH A:1425binding site for residue SAH A 1206
07AC7SOFTWARECYS B:974 , CYS B:987 , CYS B:1017 , CYS B:1021binding site for residue ZN B 1201
08AC8SOFTWARECYS B:980 , CYS B:1017 , CYS B:1023 , CYS B:1027binding site for residue ZN B 1202
09AC9SOFTWARECYS B:974 , CYS B:976 , CYS B:980 , CYS B:985binding site for residue ZN B 1203
10AD1SOFTWARECYS B:1115 , CYS B:1168 , CYS B:1170 , CYS B:1175binding site for residue ZN B 1204
11AD2SOFTWAREMET 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:1354 , HOH B:1402 , HOH B:1413binding site for residue SAM B 1205
12AD3SOFTWARETYR B:1067 , ASP B:1074 , ALA B:1077 , ASP B:1078 , LEU B:1086 , PHE B:1087 , ASP B:1088 , PHE B:1152 , TYR B:1154 , ARG B:1157 , PHE B:1158 , LYS C:4 , THR C:6 , ALA C:7 , SER C:10 , HOH C:105binding site for Di-peptide ARG C 8 and NLE C 9
13AD4SOFTWARETYR B:1067 , LEU B:1086 , PHE B:1087 , ASP B:1088 , ASN B:1091 , PHE B:1152 , TYR B:1154 , ARG C:8 , THR C:11 , GLY C:12 , HOH C:105binding site for Di-peptide NLE C 9 and SER C 10

(-) 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 5T0M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T0M)

(-) Exons   (0, 0)

(no "Exon" information available for 5T0M)

(-) 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:260
                                                                                                                                                                                                                                                                                                     
               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..............hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5t0m A  921 IICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIAL 1184
                                   930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090|     1104      1114      1124      1134      1144      1154      1164      1174      1184
                                                                                                                                                                                                  1090|                                                                                         
                                                                                                                                                                                                   1095                                                                                         


Chain B from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.............eee...........ee....ee........hhhhh.............hhhhhhh......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhh.......eee........eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh..............hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5t0m B  916 IRTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDNKDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQ 1186
                                   925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185 


Chain C 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
                5t0m C    3 TKQTARxSTG   12
                                  | 12
                                  9-NLE


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
                5t0m P    3 TKQTARxSTG   12
                                  | 12
                                  9-NLE
   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 5T0M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T0M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T0M)

(-) Gene Ontology  (51, 55)

Asymmetric Unit(hide GO term definitions)

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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 5t0k 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 5t0k 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6

(-) Related Entries Specified in the PDB File

5t0k