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(-) Description

Title :  STRUCTURAL MODEL OF SET8 HISTONE H4 LYS20 METHYLTRANSFERASE BOUND TO NUCLEOSOME CORE PARTICLE
 
Authors :  G. Tavarekere, R. K. Mcginty, S. Tan
Date :  21 Jan 16  (Deposition) - 23 Mar 16  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.50
Chains :  Asym. Unit :  A,B,G,H,I,J,K,M
Biol. Unit 1:  A,B,G,H,I,J,K,M  (2x)
Keywords :  Chromatin Enzyme, Chromatin Complex, Epigenetics, Histone Methyltransferase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Girish, R. K. Mcginty, S. Tan
Multivalent Interactions By The Set8 Histone Methyltransferase With Its Nucleosome Substrate.
J. Mol. Biol. V. 428 1531 2016
PubMed-ID: 26953260  |  Reference-DOI: 10.1016/J.JMB.2016.02.025

(-) Compounds

Molecule 1 - HISTONE H3.2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3D
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
 
Molecule 2 - HISTONE H4
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
 
Molecule 3 - HISTONE H2A
    Chains: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Gene: HIST1H2AJ, LOC494591
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
 
Molecule 4 - HISTONE H2B 1.1
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: H2B1.1
 
Molecule 5 - DNA (149-MER)
    Chains: I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLASMID
    Expression System Strain: HB101
    Expression System Taxid: 562
    Gene: WIDOM 601 NUCLEOSOME POSITIONING SEQUENCE
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
 
Molecule 6 - DNA (149-MER)
    Chains: J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLASMID
    Expression System Strain: HB101
    Expression System Taxid: 562
    Gene: WIDOM 601 NUCLEOSOME POSITIONING SEQUENCE
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
 
Molecule 7 - GUANINE NUCLEOTIDE EXCHANGE FACTOR SRM1
    Chains: K
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PST50TR
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Gene: SRM1, MTR1, PRP20, YGL097W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: PHEROMONE RESPONSE PATHWAY COMPONENT SRM1,PRE-MRNA- PROCESSING PROTEIN 20,REGULATOR OF CHROMOSOME CONDENSATION,SUPPRESSOR OF RECEPTOR MUTATIONS 1,MRNA TRANSPORT PROTEIN 1
 
Molecule 8 - N-LYSINE METHYLTRANSFERASE SETD8
    Chains: M
    EC Number: 2.1.1.-, 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PST50TR
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Gene: SETD8, KMT5A, PRSET7, SET07, SET8
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: H4-K20-HMTASE SETD8,HISTONE-LYSINE N-METHYLTRANSFERASE SETD8,LYSINE N-METHYLTRANSFERASE 5A,PR/SET DOMAIN-CONTAINING PROTEIN 07,PR/SET07,SET DOMAIN-CONTAINING PROTEIN 8

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABGHIJKM
Biological Unit 1 (2x): ABGHIJKM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5HQ2)

(-) Sites  (0, 0)

(no "Site" information available for 5HQ2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HQ2)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Asp H:48 -Thr H:49
2Thr H:49 -Gly H:50
3Glu K:102 -Ser K:103
4Pro K:266 -Arg K:267
5Pro K:268 -Phe K:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HQ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HQ2)

(-) Exons   (0, 0)

(no "Exon" information available for 5HQ2)

(-) 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:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5hq2 A  37 KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
                                    46        56        66        76        86        96       106       116       126         


Chain B from PDB  Type:PROTEIN  Length:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 5hq2 B  24 DNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFG 101
                                    33        43        53        63        73        83        93        


Chain G from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhh...ee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5hq2 G  15 KTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 119
                                    24        34        44        54        64        74        84        94       104       114     


Chain H from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5hq2 H  28 KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 122
                                    37        47        57        67        77        87        97       107       117     


Chain I from PDB  Type:DNA  Length:73
                                                                                                         
                 5hq2 I -39 TCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCGTCTCCAGGCACGTGTCAGATATATACATCCTG  72
                                   -30       -20       -10         0|       49        59        69   
                                                                   0|                                
                                                                   40                                


Chain J from PDB  Type:DNA  Length:72
                                                                                                        
                 5hq2 J -72 CAGGATGTATATATCTGACACGTGCCTGGAGACCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGA  39
                                   -63       -53       -43  ||     7        17        27        37  
                                                          -40|                                      
                                                             1                                      


Chain K from PDB  Type:PROTEIN  Length:422
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh.........ee...............................hhhhhh..eee.....eeee......eee............hhhhh.ee.......................ee........eeeee.ee.....ee........eeeeeee.....................................................eeee........eee.....................................eeeeee...eeeeee....eeeeee.................ee.....eeee...........eeee.....eeeeee....eeeee....................ee........ee............eee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hq2 K  23 KTHASHIINAQEDYKHMYLSVQPLDIFCWGTGSMCELGLGPLAKNKEVKRPRLNPFLPRDEAKIISFAVGGMHTLALDEESNVWSWGCNDVGALGRDTELESTPAKIPRESFPPLAEGHKVVQLAATDNMSCALFSNGEVYAWGTFRCNEGILGFYQDKIKIQKTPWKVPTFSKYNIVQLAPGKDHILFLDEEGMVFAWGNGQQMERFRLKTLDPRPFGLRHVKYIASGENHCFALTKDNKLVSWGLNQFGQCGVSEDVLVTKPKRLALPDNVVIRSIAAGEHHSLILSQDGDLYSCGRLDMFEVGIPKDNLPEYTYKDVHGKARAVPLPTKLNNVPKFKSVAAGSHHSVAVAQNGIAYSWGFGETYAVGLGPFEDDTEVPTRIKNTATQDHNIILVGCGGQFSVSGGVKLSDEDAEKRADE 477
                                    32        42        52        62        72        82        92       102       112       146       156       166       176       186       196       206       216       226       236       246   ||  261       271       281       291       301       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475  
                                                                                                                           120|                                                                                                      250|                                                   310|                                                                                                                                                                  
                                                                                                                            145                                                                                                       256                                                    315                                                                                                                                                                  


Chain M from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.....eeee.....eeee.........eeee............hhhhhhh.............................hhhhhee......eeee........eeee.........eeee.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hq2 M 193 KSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAFPWLKH 352
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
   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 5HQ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HQ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HQ2)

(-) Gene Ontology  (40, 68)

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  Cis Peptide Bonds
    Asp H:48 - Thr H:49   [ RasMol ]  
    Glu K:102 - Ser K:103   [ RasMol ]  
    Pro K:266 - Arg K:267   [ RasMol ]  
    Pro K:268 - Phe K:269   [ RasMol ]  
    Thr H:49 - Gly H:50   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        H2A1_XENLA | P06897: 1aoi 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2fj7 2nzd 3b6f 3b6g 3c1b 3c1c 3kuy 3kwq 3lja 3mnn 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4j8u 4j8v 4j8w 4j8x 4ld9 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5cp6 5dnm 5dnn 5e5a 5f99 5g2e 5mlu 5nl0
        H2B11_XENLA | P02281: 1aoi 1f66 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2nzd 3b6f 3b6g 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4j8u 4j8v 4j8w 4j8x 4kgc 4kha 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5cp6 5dnm 5dnn 5e5a 5f99 5g2e 5nl0 5x0x 5x0y
        H32_XENLA | P84233: 1f66 1kx3 1kx4 1kx5 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2hue 2io5 2nzd 3b6f 3b6g 3c1b 3c1c 3gv6 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4eo5 4j8u 4j8v 4j8w 4j8x 4kgc 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5e5a 5f99 5kgf 5mlu 5nl0 5x0x 5x0y
        H4_XENLA | P62799: 1aoi 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2hue 2io5 2nzd 3b6f 3b6g 3c1b 3c1c 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4eo5 4j8u 4j8v 4j8w 4j8x 4kgc 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zbj 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5e5a 5f99 5kgf 5mlu 5nl0 5x0x 5x0y
        KMT5A_HUMAN | Q9NQR1: 1zkk 2bqz 3f9w 3f9x 3f9y 3f9z 4ij8 5t5g 5teg 5th7 5w1y
        Q6AZJ8_XENLA | Q6AZJ8: 2nzd 3b6f 3b6g 3kuy 3kwq 3lja 3mnn 3tu4 3ut9 3uta 3utb 4j8v 4j8w 4j8x 4ld9 4xuj 4xzq 4ys3 4z66 5cp6 5dnm 5dnn 5e5a
        RCC1_YEAST | P21827: 3of7 4oih
UniProtKB/TrEMBL
        Q6AZJ8_XENLA | Q6AZJ8: 3kxb 3lel 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mvd 4kgc 4kha 4r8p 5x0x 5x0y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5HQ2)