eF-site ID 3w98-ABCDEFGHIJ
PDB Code 3w98
Chain A, B, C, D, E, F, G, H, I, J

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Title Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region
Classification STRUCTURAL PROTEIN/DNA
Compound Histone H3.1
Source Homo sapiens (Human) (3W98)
Sequence A:  PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQD
FKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRV
TIMPKDIQLARRIRGER
B:  NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLEN
VIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF
C:  KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLA
AVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEE
LNKLLGRVTIAQGGVLPNIQAVLLPK
D:  KRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDI
FERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKH
AVSEGTKAVTKYTSA
E:  KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQ
DFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA
F:  RKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVL
KVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY
GFGG
G:  KTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAV
LEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELN
KLLGRVTIAQGGVLPNIQAVLLPK
H:  RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFER
IAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVS
EGTKAVTKYTS
I:  ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGG
AAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCT
GAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGA
J:  ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGG
AAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCT
GAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT
Description


Functional site

1) chain D
residue 48
type
sequence V
description BINDING SITE FOR RESIDUE MN E 1001
source : AC1

2) chain E
residue 77
type
sequence D
description BINDING SITE FOR RESIDUE MN E 1001
source : AC1

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

4) chain D
residue 92-114
type prosite
sequence REIQTAVRLLLPGELAKHAVSEG
description HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
source prosite : PS00357

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

6) chain D
residue 36
type MOD_RES
sequence S
description Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q64475
source Swiss-Prot : SWS_FT_FI10

7) chain H
residue 36
type MOD_RES
sequence S
description Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q64475
source Swiss-Prot : SWS_FT_FI10

8) chain D
residue 46
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000269|PubMed:16627869
source Swiss-Prot : SWS_FT_FI11

9) chain D
residue 108
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000269|PubMed:16627869
source Swiss-Prot : SWS_FT_FI11

10) chain H
residue 46
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000269|PubMed:16627869
source Swiss-Prot : SWS_FT_FI11

11) chain H
residue 108
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000269|PubMed:16627869
source Swiss-Prot : SWS_FT_FI11

12) chain D
residue 57
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269|PubMed:24681537
source Swiss-Prot : SWS_FT_FI12

13) chain H
residue 57
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269|PubMed:24681537
source Swiss-Prot : SWS_FT_FI12

14) chain D
residue 79
type MOD_RES
sequence R
description Dimethylated arginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI13

15) chain H
residue 79
type MOD_RES
sequence R
description Dimethylated arginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI13

16) chain D
residue 86
type MOD_RES
sequence R
description Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI14

17) chain D
residue 92
type MOD_RES
sequence R
description Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI14

18) chain H
residue 86
type MOD_RES
sequence R
description Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI14

19) chain H
residue 92
type MOD_RES
sequence R
description Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI14

20) chain D
residue 115
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q00729
source Swiss-Prot : SWS_FT_FI15

21) chain H
residue 115
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q00729
source Swiss-Prot : SWS_FT_FI15

22) chain F
residue 91
type MOD_RES
sequence K
description Phosphothreonine => ECO:0000250|UniProtKB:Q00729
source Swiss-Prot : SWS_FT_FI15

23) chain D
residue 112
type CARBOHYD
sequence S
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

24) chain H
residue 112
type CARBOHYD
sequence S
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

25) chain B
residue 79
type CARBOHYD
sequence K
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

26) chain F
residue 20
type CARBOHYD
sequence K
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

27) chain F
residue 59
type CARBOHYD
sequence K
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

28) chain F
residue 79
type CARBOHYD
sequence K
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

29) chain D
residue 120
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:16713563
source Swiss-Prot : SWS_FT_FI18

30) chain H
residue 120
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:16713563
source Swiss-Prot : SWS_FT_FI18

31) chain D
residue 34
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816
source Swiss-Prot : SWS_FT_FI20

32) chain H
residue 34
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816
source Swiss-Prot : SWS_FT_FI20

33) chain H
residue 43
type MOD_RES
sequence K
description N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732
source Swiss-Prot : SWS_FT_FI3

34) chain H
residue 85
type MOD_RES
sequence K
description N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732
source Swiss-Prot : SWS_FT_FI3

35) chain D
residue 43
type MOD_RES
sequence K
description N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732
source Swiss-Prot : SWS_FT_FI3

36) chain D
residue 85
type MOD_RES
sequence K
description N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732
source Swiss-Prot : SWS_FT_FI3

37) chain G
residue 95
type MOD_RES
sequence K
description ADP-ribosylserine => ECO:0000269|PubMed:34874266
source Swiss-Prot : SWS_FT_FI4

38) chain B
residue 44
type MOD_RES
sequence K
description N6-crotonyllysine; alternate => ECO:0000269|PubMed:21925322
source Swiss-Prot : SWS_FT_FI5

39) chain F
residue 44
type MOD_RES
sequence K
description N6-crotonyllysine; alternate => ECO:0000269|PubMed:21925322
source Swiss-Prot : SWS_FT_FI5

40) chain B
residue 77
type MOD_RES
sequence K
description Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711
source Swiss-Prot : SWS_FT_FI6

41) chain B
residue 91
type MOD_RES
sequence K
description Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711
source Swiss-Prot : SWS_FT_FI6

42) chain F
residue 31
type MOD_RES
sequence K
description Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711
source Swiss-Prot : SWS_FT_FI6

43) chain F
residue 77
type MOD_RES
sequence K
description Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711
source Swiss-Prot : SWS_FT_FI6

44) chain F
residue 91
type MOD_RES
sequence K
description Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711
source Swiss-Prot : SWS_FT_FI6

45) chain G
residue 74
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:24681537
source Swiss-Prot : SWS_FT_FI7

46) chain G
residue 75
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:24681537
source Swiss-Prot : SWS_FT_FI7

47) chain D
residue 34
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

48) chain D
residue 116
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

49) chain D
residue 120
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

50) chain H
residue 34
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

51) chain H
residue 116
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

52) chain H
residue 120
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

53) chain D
residue 35
type MOD_RES
sequence E
description PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475
source Swiss-Prot : SWS_FT_FI9

54) chain H
residue 35
type MOD_RES
sequence E
description PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475
source Swiss-Prot : SWS_FT_FI9

55) chain G
residue 118
type MOD_RES
sequence K
description PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475
source Swiss-Prot : SWS_FT_FI9


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