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(-) Description

Title :  HUMAN NUCLEOSOME CONTAINING CPG METHYLATED DNA
 
Authors :  Y. Fujii, M. Wakamori, T. Umehara, S. Yokoyama
Date :  18 Jan 16  (Deposition) - 15 Jun 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Chromatin, Epigenetics, Histone, Transcription, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fujii, M. Wakamori, T. Umehara, S. Yokoyama
Crystal Structure Of Human Nucleosome Core Particle Containing Enzymatically Introduced Cpg Methylation
Febs Open Bio V. 6 498 2016
PubMed: search  |  Reference-DOI: 10.1002/2211-5463.12064

(-) Compounds

Molecule 1 - HISTONE H3.1
    Chains: A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Expression System Vector Type: PLASMID
    Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H3/A,HISTONE H3/B,HISTONE H3/C,HISTONE H3/D,HISTONE H3/F,HISTONE H3/H,HISTONE H3/I,HISTONE H3/J,HISTONE H3/K,HISTONE H3/L
 
Molecule 2 - HISTONE H4
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Expression System Vector Type: PLASMID
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - HISTONE H2A TYPE 1-B/E
    Chains: C, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Expression System Vector Type: PLASMID
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H2A.2,HISTONE H2A/A,HISTONE H2A/M
 
Molecule 4 - HISTONE H2B TYPE 1-J
    Chains: D, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Expression System Vector Type: PLASMID
    Gene: HIST1H2BJ, H2BFR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H2B.1,HISTONE H2B.R,H2B/R
 
Molecule 5 - DNA (146-MER)
    Chains: I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI HB101
    Expression System Strain: HB101
    Expression System Taxid: 634468
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
15CM8Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2MN7Ligand/IonMANGANESE (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL D:45 , HOH D:201 , ASP E:77binding site for residue MN E 301
2AC2SOFTWAREDT I:13binding site for residue MN I 101
3AC3SOFTWAREDG I:48binding site for residue MN I 102
4AC4SOFTWAREDG I:27 , HOH I:205binding site for residue MN I 103
5AC5SOFTWAREDT I:67 , DG J:26binding site for residue MN J 101
6AC6SOFTWAREDG J:-3binding site for residue MN J 102
7AC7SOFTWAREDG J:47binding site for residue MN J 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B2J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5B2J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B2J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B2J)

(-) Exons   (0, 0)

(no "Exon" information available for 5B2J)

(-) 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:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5b2j A  37 KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
                                    46        56        66        76        86        96       106       116       126         


Chain B from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 5b2j B  21 VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    30        40        50        60        70        80        90       100  


Chain C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh...hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 5b2j C  13 KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK 118
                                    22        32        42        52        62        72        82        92       102       112      


Chain D from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5b2j D  26 RKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 122
                                    35        45        55        65        75        85        95       105       115       


Chain E from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5b2j E  37 KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
                                    46        56        66        76        86        96       106       116       126         


Chain F from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 5b2j F  18 HRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    27        37        47        57        67        77        87        97     


Chain G from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...hhhhhhhhhhh.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5b2j G  14 AKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK 118
                                    23        33        43        53        63        73        83        93       103       113     


Chain H from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5b2j H  28 RSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA 121
                                    37        47        57        67        77        87        97       107       117    


Chain I from PDB  Type:DNA  Length:146
                                                                                                                                                                                  
                 5b2j I -72 ATCAATATCCAxGTGCCAGTTATACCAAAAGTGTATTTGGAAACTCCTAACTGAAAAGGCATGTTCAxGTGAATTCAxGTGAACATGCCTTTTCAGTTAGGAGTTTCCAAATACACTTTTGGTATAACTGGCAxGTGGATATTGAT  73
                                   -63 |     -53       -43       -33       -23       -13       |-3       | 7        17        27        37        47        57   |    67      
                                     -61-5CM                                                  -5-5CM     5-5CM                                                  61-5CM        


Chain J from PDB  Type:DNA  Length:146
                                                                                                                                                                                  
                 5b2j J -73 ATCAATATCCAxGTGCCAGTTATACCAAAAGTGTATTTGGAAACTCCTAACTGAAAAGGCATGTTCAxGTGAATTCAxGTGAACATGCCTTTTCAGTTAGGAGTTTCCAAATACACTTTTGGTATAACTGGCAxGTGGATATTGAT  72
                                   -64 |     -54       -44       -34       -24       -14       |-4       | 6        16        26        36        46        56   |    66      
                                     -62-5CM                                                  -6-5CM     4-5CM                                                  60-5CM
   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 5B2J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B2J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B2J)

(-) Gene Ontology  (45, 82)

Asymmetric/Biological Unit(hide GO term definitions)

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  5b2j
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  H2A1B_HUMAN | P04908
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  H2B1J_HUMAN | P06899
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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
        H2A1B_HUMAN | P04908: 2cv5 2rvq 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3w96 3w97 3w98 3w99 3wkj 3wtp 3x1s 3x1v 4ym5 4ym6 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b31 5b32 5b40 5cpi 5cpj 5cpk 5gse 5gtc 5gxq 5jrg 5vey 5x7x
        H2B1J_HUMAN | P06899: 2rvq 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3w96 3w97 3w98 3w99 3wa9 3waa 3wtp 4cay 4ym5 4ym6 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b31 5b32 5b33 5b40 5cpi 5cpj 5cpk 5fug 5gse 5gtc 5gxq 5jrg 5vey 5x7x
        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 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 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
        H4_HUMAN | P62805: 1kx4 1kx5 1m18 1m19 1m1a 1s32 1zkk 2bqz 2cv5 2ig0 2kwn 2kwo 2lvm 2qqs 2rje 2rny 2rs9 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3cfs 3cfv 3f9w 3f9x 3f9y 3f9z 3ij1 3jpx 3nqj 3nqu 3o36 3qby 3qzs 3qzt 3qzv 3r45 3uvw 3uvx 3uvy 3uw9 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4gqb 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4m38 4n3w 4n4f 4qut 4quu 4qyd 4u9w 4ym5 4ym6 4yy6 4yyd 4yyg 4yyh 4yyi 4yyj 4yyk 4yym 4yyn 4z2m 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b31 5b32 5b33 5b40 5bnv 5bnx 5bo0 5c3i 5cpi 5cpj 5cpk 5fa5 5ffw 5fwe 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5ja4 5jrg 5kdm 5teg 5x7x

(-) Related Entries Specified in the PDB File

5b2i