eF-site ID 5onw-ABCDEFGHIJ
PDB Code 5onw
Chain A, B, C, D, E, F, G, H, I, J

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Title X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C
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:  KTRSSRAGLQFPVGRVHRLLRKGCYAERVGAGAPVYLAAV
LEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELN
KLLGRVTIAQGGVLPNIQSVLLP
D:  RRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVND
VFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAK
HAVSEGTKAVTKYTSA
E:  HCYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF
KTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVT
IMPKDIQLARRIRGE
F:  RHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT
LYGFGG
G:  AKTRSSRAGLQFPVGRVHRLLRKGCYAERVGAGAPVYLAA
VLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEEL
NKLLGRVTIAQGGVLPNIQSVLLPK
H:  RKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFER
IAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVS
EGTKAVTKYTSA
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 48
type
sequence G
description binding site for residue MN I 103
source : AC3

6) chain I
residue 49
type
sequence G
description binding site for residue MN I 103
source : AC3

7) chain I
residue 61
type
sequence G
description binding site for residue MN I 104
source : AC4

8) chain I
residue -35
type
sequence G
description binding site for residue MN I 105
source : AC5

9) chain I
residue -34
type
sequence G
description binding site for residue MN I 105
source : AC5

10) chain I
residue 27
type
sequence G
description binding site for residue MN I 106
source : AC6

11) chain I
residue 64
type
sequence G
description binding site for residue MN I 107
source : AC7

12) chain I
residue 65
type
sequence G
description binding site for residue MN I 107
source : AC7

13) chain I
residue -2
type
sequence G
description binding site for residue MN I 108
source : AC8

14) chain I
residue -3
type
sequence G
description binding site for residue MN I 108
source : AC8

15) chain I
residue 4
type
sequence A
description binding site for residue MN I 109
source : AC9

16) chain I
residue 5
type
sequence G
description binding site for residue MN I 109
source : AC9

17) chain J
residue 70
type
sequence X
description binding site for residue MN J 101
source : AD1

18) chain J
residue 71
type
sequence G
description binding site for residue MN J 101
source : AD1

19) chain J
residue -58
type
sequence G
description binding site for residue MN J 102
source : AD2

20) chain J
residue -59
type
sequence G
description binding site for residue MN J 102
source : AD2

21) chain J
residue 48
type
sequence G
description binding site for residue MN J 103
source : AD3

22) chain J
residue 27
type
sequence G
description binding site for residue MN J 104
source : AD4

23) chain J
residue -3
type
sequence G
description binding site for residue MN J 105
source : AD5

24) chain J
residue 61
type
sequence G
description binding site for residue MN J 106
source : AD6

25) chain J
residue -35
type
sequence G
description binding site for residue MN J 107
source : AD7

26) chain J
residue -34
type
sequence G
description binding site for residue MN J 107
source : AD7

27) chain J
residue 4
type
sequence A
description binding site for residue MN J 108
source : AD8

28) chain J
residue 5
type
sequence G
description binding site for residue MN J 108
source : AD8

29) chain J
residue 59
type
sequence C
description binding site for residue MN J 109
source : AD9

30) chain A
residue 120
type
sequence M
description binding site for residue CL A 201
source : AE1

31) chain A
residue 121
type
sequence P
description binding site for residue CL A 201
source : AE1

32) chain A
residue 122
type
sequence K
description binding site for residue CL A 201
source : AE1

33) chain C
residue 44
type
sequence G
description binding site for residue CL C 201
source : AE2

34) chain C
residue 46
type
sequence G
description binding site for residue CL C 201
source : AE2

35) chain C
residue 47
type
sequence A
description binding site for residue CL C 201
source : AE2

36) chain D
residue 87
type
sequence T
description binding site for residue CL C 201
source : AE2

37) chain D
residue 88
type
sequence S
description binding site for residue CL C 201
source : AE2

38) chain D
residue 120
type
sequence S
description binding site for residue MN D 201
source : AE3

39) chain D
residue 45
type
sequence V
description binding site for residue MN E 201
source : AE4

40) chain E
residue 77
type
sequence D
description binding site for residue MN E 201
source : AE4

41) chain E
residue 121
type
sequence P
description binding site for residue CL E 202
source : AE5

42) chain E
residue 122
type
sequence K
description binding site for residue CL E 202
source : AE5

43) chain G
residue 44
type
sequence G
description binding site for residue CL G 201
source : AE6

44) chain G
residue 46
type
sequence G
description binding site for residue CL G 201
source : AE6

45) chain G
residue 47
type
sequence A
description binding site for residue CL G 201
source : AE6

46) chain H
residue 87
type
sequence T
description binding site for residue CL G 201
source : AE6

47) chain H
residue 88
type
sequence S
description binding site for residue CL G 201
source : AE6

48) chain E
residue 39
type
sequence H
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

49) chain E
residue 41
type
sequence Y
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

50) chain E
residue 42
type
sequence R
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

51) chain E
residue 66
type
sequence P
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

52) chain E
residue 67
type
sequence F
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

53) chain E
residue 68
type
sequence Q
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

54) chain E
residue 69
type
sequence R
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

55) chain E
residue 71
type
sequence V
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

56) chain E
residue 72
type
sequence R
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

57) chain E
residue 73
type
sequence E
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

58) chain E
residue 74
type
sequence I
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

59) chain F
residue 26
type
sequence I
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

60) chain I
residue -39
type
sequence A
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

61) chain I
residue -41
type
sequence G
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

62) chain I
residue -40
type
sequence T
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

63) chain I
residue -69
type
sequence A
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

64) chain I
residue -70
type
sequence C
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

65) chain J
residue 39
type
sequence T
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

66) chain J
residue 41
type
sequence C
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

67) chain J
residue 69
type
sequence T
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

68) chain J
residue 71
type
sequence G
description binding site for Di-peptide CYS E 40 and G47 J 70
source : AE7

69) chain C
residue 21-27
type prosite
sequence AGLQFPV
description HISTONE_H2A Histone H2A signature. AGLqFPV
source prosite : PS00046

70) chain D
residue 89-111
type prosite
sequence REIQTAVRLLLPGELAKHAVSEG
description HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
source prosite : PS00357

71) chain A
residue 66-74
type prosite
sequence PFQRLVREI
description HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
source prosite : PS00959

72) chain B
residue 59
type MOD_RES
sequence K
description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805
source Swiss-Prot : SWS_FT_FI10

73) chain E
residue 64
type MOD_RES
sequence K
description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805
source Swiss-Prot : SWS_FT_FI10

74) chain F
residue 59
type MOD_RES
sequence K
description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805
source Swiss-Prot : SWS_FT_FI10

75) chain A
residue 64
type MOD_RES
sequence K
description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805
source Swiss-Prot : SWS_FT_FI10

76) chain B
residue 77
type MOD_RES
sequence K
description N6-succinyllysine => ECO:0000250|UniProtKB:P62805
source Swiss-Prot : SWS_FT_FI11

77) chain F
residue 77
type MOD_RES
sequence K
description N6-succinyllysine => ECO:0000250|UniProtKB:P62805
source Swiss-Prot : SWS_FT_FI11

78) 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

79) 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

80) 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

81) 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

82) chain A
residue 41
type MOD_RES
sequence Y
description Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI14

83) chain E
residue 41
type MOD_RES
sequence Y
description Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI14

84) chain A
residue 56
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228
source Swiss-Prot : SWS_FT_FI15

85) chain A
residue 79
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228
source Swiss-Prot : SWS_FT_FI15

86) chain E
residue 56
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228
source Swiss-Prot : SWS_FT_FI15

87) chain E
residue 79
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228
source Swiss-Prot : SWS_FT_FI15

88) chain A
residue 57
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI16

89) chain E
residue 57
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI16

90) chain A
residue 80
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI17

91) chain A
residue 107
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI17

92) chain E
residue 80
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI17

93) chain E
residue 107
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI17

94) chain A
residue 86
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI18

95) chain E
residue 86
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI18

96) chain A
residue 115
type MOD_RES
sequence K
description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI19

97) chain E
residue 115
type MOD_RES
sequence K
description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI19

98) chain A
residue 122
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI20

99) chain E
residue 122
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI20

100) chain A
residue 110
type LIPID
sequence A
description S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI21

101) chain E
residue 110
type LIPID
sequence A
description S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI21

102) chain C
residue 95
type MOD_RES
sequence K
description N6-succinyllysine => ECO:0000250|UniProtKB:P0C0S8
source Swiss-Prot : SWS_FT_FI3

103) chain G
residue 95
type MOD_RES
sequence K
description N6-succinyllysine => ECO:0000250|UniProtKB:P0C0S8
source Swiss-Prot : SWS_FT_FI3

104) 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

105) 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

106) 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

107) chain C
residue 74
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8
source Swiss-Prot : SWS_FT_FI5

108) chain C
residue 75
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8
source Swiss-Prot : SWS_FT_FI5

109) chain G
residue 74
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8
source Swiss-Prot : SWS_FT_FI5

110) chain G
residue 75
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8
source Swiss-Prot : SWS_FT_FI5

111) chain F
residue 44
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8
source Swiss-Prot : SWS_FT_FI5

112) chain F
residue 79
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8
source Swiss-Prot : SWS_FT_FI5

113) chain C
residue 104
type MOD_RES
sequence Q
description N5-methylglutamine => ECO:0000250
source Swiss-Prot : SWS_FT_FI6

114) chain G
residue 104
type MOD_RES
sequence Q
description N5-methylglutamine => ECO:0000250
source Swiss-Prot : SWS_FT_FI6

115) chain F
residue 20
type MOD_RES
sequence K
description N5-methylglutamine => ECO:0000250
source Swiss-Prot : SWS_FT_FI6

116) chain G
residue 118
type MOD_RES
sequence K
description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8
source Swiss-Prot : SWS_FT_FI7

117) chain F
residue 31
type MOD_RES
sequence K
description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8
source Swiss-Prot : SWS_FT_FI7

118) chain F
residue 91
type MOD_RES
sequence K
description N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8
source Swiss-Prot : SWS_FT_FI7

119) 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

120) 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

121) 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

122) chain B
residue 51
type MOD_RES
sequence Y
description Phosphotyrosine => ECO:0000250|UniProtKB:P62805
source Swiss-Prot : SWS_FT_FI9

123) chain B
residue 88
type MOD_RES
sequence Y
description Phosphotyrosine => ECO:0000250|UniProtKB:P62805
source Swiss-Prot : SWS_FT_FI9

124) chain F
residue 51
type MOD_RES
sequence Y
description Phosphotyrosine => ECO:0000250|UniProtKB:P62805
source Swiss-Prot : SWS_FT_FI9

125) 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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