eF-site ID 5ong-ABCDEFGHIJ PDB Code 5ong Chain A, B, C, D, E, F, G, H, I, J click to enlarge Title X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer Classification DNA BINDING PROTEIN Compound DNA (147-MER) Source Xenopus laevis (African clawed frog) (H2B11_XENLA) Sequence A:  HCYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF KTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVT IMPKDIQLARRIRGER B:  NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLEN VIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG C:  KTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAV LEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELN KLLGRVTIAQGGVLPNIQSVLLPKKT D:  KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVF ERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHA VSEGTKAVTKYTSA E:  HCYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF KTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVT IMPKDIQLARRIRGERA F:  RKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVL KVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY GFGG G:  AKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAA VLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEEL NKLLGRVTIAQGGVLPNIQSVLLPKK H:  TRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFE RIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAV SEGTKAVTKYTSA I:  ATCCATATCCACCTGGTCCTACTACCAAAAGTGTATTTGG AAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGC TGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTT TGGTAGTAGGACCAGGTGGATATXGAT J:  ATCCATATCCACCTGGTCCTACTACCAAAAGTGTATTTGG AAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGC TGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTT TGGTAGTAGGACCAGGTGGATATXGAT Description Functional site 1) chain I residue 70 type sequence X description binding site for residue MN I 101 source : AC1 2) chain I residue 71 type sequence G description binding site for residue MN I 101 source : AC1 3) chain I residue -59 type sequence G description binding site for residue MN I 102 source : AC2 4) chain I residue -58 type sequence G description binding site for residue MN I 102 source : AC2 5) chain I residue 55 type sequence G description binding site for residue MN I 103 source : AC3 6) chain I residue 56 type sequence G description binding site for residue MN I 103 source : AC3 7) chain I residue 47 type sequence T description binding site for residue MN I 105 source : AC4 8) chain I residue 48 type sequence G description binding site for residue MN I 105 source : AC4 9) chain I residue 61 type sequence G description binding site for residue MN I 106 source : AC5 10) chain I residue 27 type sequence G description binding site for residue MN I 107 source : AC6 11) chain I residue 5 type sequence G description binding site for residue MN I 108 source : AC7 12) chain I residue -3 type sequence G description binding site for residue MN I 109 source : AC8 13) chain I residue -2 type sequence G description binding site for residue MN I 109 source : AC8 14) chain I residue -35 type sequence G description binding site for residue MN I 110 source : AC9 15) chain I residue -34 type sequence G description binding site for residue MN I 110 source : AC9 16) chain J residue -59 type sequence G description binding site for residue MN J 101 source : AD1 17) chain J residue -16 type sequence G description binding site for residue MN J 102 source : AD2 18) chain J residue -35 type sequence G description binding site for residue MN J 103 source : AD3 19) chain J residue -34 type sequence G description binding site for residue MN J 103 source : AD3 20) chain J residue 70 type sequence X description binding site for residue MN J 104 source : AD4 21) chain J residue 71 type sequence G description binding site for residue MN J 104 source : AD4 22) chain J residue 61 type sequence G description binding site for residue MN J 106 source : AD5 23) chain J residue 27 type sequence G description binding site for residue MN J 107 source : AD6 24) chain J residue -3 type sequence G description binding site for residue MN J 108 source : AD7 25) chain J residue 48 type sequence G description binding site for residue MN J 109 source : AD8 26) chain A residue 121 type sequence P description binding site for residue CL A 201 source : AD9 27) chain A residue 122 type sequence K description binding site for residue CL A 201 source : AD9 28) chain C residue 46 type sequence G description binding site for residue CL D 201 source : AE1 29) chain D residue 87 type sequence T description binding site for residue CL D 201 source : AE1 30) chain D residue 88 type sequence S description binding site for residue CL D 201 source : AE1 31) chain D residue 45 type sequence V description binding site for residue MN E 201 source : AE2 32) chain E residue 77 type sequence D description binding site for residue MN E 201 source : AE2 33) chain E residue 121 type sequence P description binding site for residue CL E 202 source : AE3 34) chain E residue 122 type sequence K description binding site for residue CL E 202 source : AE3 35) chain G residue 44 type sequence G description binding site for residue CL G 201 source : AE4 36) chain G residue 46 type sequence G description binding site for residue CL G 201 source : AE4 37) chain H residue 87 type sequence T description binding site for residue CL G 201 source : AE4 38) chain H residue 88 type sequence S description binding site for residue CL G 201 source : AE4 39) chain E residue 39 type sequence H description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 40) chain E residue 41 type sequence Y description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 41) chain E residue 66 type sequence P description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 42) chain E residue 67 type sequence F description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 43) chain E residue 68 type sequence Q description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 44) chain E residue 69 type sequence R description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 45) chain E residue 71 type sequence V description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 46) chain E residue 72 type sequence R description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 47) chain E residue 73 type sequence E description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 48) chain E residue 74 type sequence I description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 49) chain F residue 26 type sequence I description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 50) chain F residue 29 type sequence I description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 51) chain F residue 62 type sequence L description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 52) chain I residue -39 type sequence A description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 53) chain I residue -41 type sequence G description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 54) chain I residue -40 type sequence T description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 55) chain I residue -69 type sequence A description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 56) chain I residue -70 type sequence C description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 57) chain J residue 39 type sequence T description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 58) chain J residue 41 type sequence C description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 59) chain J residue 69 type sequence T description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 60) chain J residue 71 type sequence G description binding site for Di-peptide CYS E 40 and G47 J 70 source : AE5 61) chain C residue 21-27 type prosite sequence AGLQFPV description HISTONE_H2A Histone H2A signature. AGLqFPV source prosite : PS00046 62) chain D residue 89-111 type prosite sequence REIQTAVRLLLPGELAKHAVSEG description HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG source prosite : PS00357 63) chain A residue 66-74 type prosite sequence PFQRLVREI description HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI source prosite : PS00959 64) chain B residue 59 type MOD_RES sequence K description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI10 65) chain E residue 64 type MOD_RES sequence K description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI10 66) chain F residue 59 type MOD_RES sequence K description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI10 67) chain A residue 64 type MOD_RES sequence K description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI10 68) chain B residue 77 type MOD_RES sequence K description N6-succinyllysine => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI11 69) chain F residue 77 type MOD_RES sequence K description N6-succinyllysine => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI11 70) chain B residue 31 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI12 71) chain F residue 31 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI12 72) chain B residue 91 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI13 73) chain F residue 91 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI13 74) chain A residue 41 type MOD_RES sequence Y description Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI14 75) chain E residue 41 type MOD_RES sequence Y description Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI14 76) chain A residue 56 type MOD_RES sequence K description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228 source Swiss-Prot : SWS_FT_FI15 77) chain A residue 79 type MOD_RES sequence K description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228 source Swiss-Prot : SWS_FT_FI15 78) chain E residue 56 type MOD_RES sequence K description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228 source Swiss-Prot : SWS_FT_FI15 79) chain E residue 79 type MOD_RES sequence K description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228 source Swiss-Prot : SWS_FT_FI15 80) chain A residue 57 type MOD_RES sequence S description Phosphoserine => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI16 81) chain E residue 57 type MOD_RES sequence S description Phosphoserine => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI16 82) chain A residue 80 type MOD_RES sequence T description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI17 83) chain A residue 107 type MOD_RES sequence T description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI17 84) chain E residue 80 type MOD_RES sequence T description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI17 85) chain E residue 107 type MOD_RES sequence T description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI17 86) chain A residue 86 type MOD_RES sequence S description Phosphoserine => ECO:0000250|UniProtKB:P84243 source Swiss-Prot : SWS_FT_FI18 87) chain E residue 86 type MOD_RES sequence S description Phosphoserine => ECO:0000250|UniProtKB:P84243 source Swiss-Prot : SWS_FT_FI18 88) chain A residue 115 type MOD_RES sequence K description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI19 89) chain E residue 115 type MOD_RES sequence K description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI19 90) chain A residue 122 type MOD_RES sequence K description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI20 91) chain E residue 122 type MOD_RES sequence K description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI20 92) chain A residue 110 type LIPID sequence A description S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI21 93) chain E residue 110 type LIPID sequence A description S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3 source Swiss-Prot : SWS_FT_FI21 94) chain C residue 95 type MOD_RES sequence K description N6-succinyllysine => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI3 95) chain G residue 95 type MOD_RES sequence K description N6-succinyllysine => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI3 96) chain C residue 36 type MOD_RES sequence K description N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI4 97) chain G residue 36 type MOD_RES sequence K description N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI4 98) chain H residue 117 type MOD_RES sequence K description N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI4 99) chain C residue 74 type MOD_RES sequence K description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI5 100) chain C residue 75 type MOD_RES sequence K description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI5 101) chain G residue 74 type MOD_RES sequence K description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI5 102) chain G residue 75 type MOD_RES sequence K description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI5 103) chain F residue 44 type MOD_RES sequence K description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI5 104) chain F residue 79 type MOD_RES sequence K description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI5 105) chain C residue 104 type MOD_RES sequence Q description N5-methylglutamine => ECO:0000250 source Swiss-Prot : SWS_FT_FI6 106) chain G residue 104 type MOD_RES sequence Q description N5-methylglutamine => ECO:0000250 source Swiss-Prot : SWS_FT_FI6 107) chain F residue 20 type MOD_RES sequence K description N5-methylglutamine => ECO:0000250 source Swiss-Prot : SWS_FT_FI6 108) chain C residue 118 type MOD_RES sequence K description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI7 109) chain G residue 118 type MOD_RES sequence K description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI7 110) chain F residue 31 type MOD_RES sequence K description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI7 111) chain F residue 91 type MOD_RES sequence K description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8 source Swiss-Prot : SWS_FT_FI7 112) chain F residue 47 type CROSSLNK sequence S description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250 source Swiss-Prot : SWS_FT_FI8 113) chain C residue 15 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250 source Swiss-Prot : SWS_FT_FI8 114) chain C residue 119 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250 source Swiss-Prot : SWS_FT_FI8 115) chain G residue 15 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250 source Swiss-Prot : SWS_FT_FI8 116) chain G residue 119 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250 source Swiss-Prot : SWS_FT_FI8 117) chain B residue 51 type MOD_RES sequence Y description Phosphotyrosine => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI9 118) chain B residue 88 type MOD_RES sequence Y description Phosphotyrosine => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI9 119) chain F residue 51 type MOD_RES sequence Y description Phosphotyrosine => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI9 120) chain F residue 88 type MOD_RES sequence Y description Phosphotyrosine => ECO:0000250|UniProtKB:P62805 source Swiss-Prot : SWS_FT_FI9

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