BMRB Entry 51141

Name: H3 tail in 145-bp nucleosome
Published: 2023-03-10

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51141

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

H3 tail in 145-bp nucleosome

Deposition date:

2021-10-14

Original release date:

2023-03-10

Authors:

Ohtomo, Hideaki

Citation:

Citation: Ohtomo, Hideaki; Ito, Shinsuke; McKenzie, Nicholas; Uckelmann, Michael; Wakamori, Masatoshi; Ehara, Haruhiko; Furukawa, Ayako; Tsunaka, Yasuo; Shibata, Marika; Sekine, Shun-Ichi; Umehara, Takashi; Davidovich, Chen; Koseki, Haruhiko; Nishimura, Yoshifumi. "H2A Ubiquitination Alters H3-tail Dynamics on Linker-DNA to Enhance H3K27 Methylation" J. Mol. Biol. 435, 167936-167936 (2023).
PubMed: 36610636

Assembly members:

Assembly members:
entity_1, polymer, 135 residues, Formula weight is not available
entity_2, polymer, 133 residues, Formula weight is not available
entity_3, polymer, 129 residues, Formula weight is not available
entity_4, polymer, 102 residues, Formula weight is not available
entity_5, polymer, 145 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: ARTKQTARKSTGGKAPRKQL ATKAARKSAPATGGVKKPHR YRPGTVALREIRRYQKSTEL LIRKLPFQRLVREIAQDFKT DLRFQSSAVMALQEACEAYL VGLFEDTNLCAIHAKRVTIM PKDIQLARRIRGERA
entity_2: GPGMSGRGKQGGKARAKAKT RSSRAGLQFPVGRVHRLLRK GNYSERVGAGAPVYLAAVLE YLTAEILELAGNAARDNKKT RIIPRHLQLAIRNDEELNKL LGRVTIAQGGVLPNIQAVLL PKKTESHHKAKGK
entity_3: GPGMPEPAKSAPAPKKGSKK AVTKAQKKDGKKRKRSRKES YSIYVYKVLKQVHPDTGISS KAMGIMNSFVNDIFERIAGE ASRLAHYNKRSTITSREIQT AVRLLLPGELAKHAVSEGTK AVTKYTSAK
entity_4: SGRGKGGKGLGKGGAKRHRK VLRDNIQGITKPAIRRLARR GGVKRISGLIYEETRGVLKV FLENVIRDAVTYTEHAKRKT VTAMDVVYALKRQGRTLYGF GG
entity_5: ATCAGAATCCCGGTGCCGAG GCCGCTCAATTGGTCGTAGA CAGCTCTAGCACCGCTTAAA CGCACGTACGCGCTGTCCCC CGCGTTTTAACCGCCAAGGG GATTACTCCCTAGTCTCCAG GCACGTGTCAGATATATACA TCGAT

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	126
15N chemical shifts	148
1H chemical shifts	148

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	nucleosome, H3	1
2	nucleosome, H2A	2
3	nucleosome, H2B	3
4	nucleosome, H4	4
5	DNA	5

Entities:

Entity 1, nucleosome, H3 135 residues - Formula weight is not available

1

ALA

ARG

THR

LYS

GLN

THR

ALA

ARG

LYS

SER

2

THR

GLY

LYS

ALA

PRO

ARG

LYS

GLN

LEU

3

ALA

THR

LYS

ALA

ARG

LYS

SER

ALA

PRO

4

ALA

THR

GLY

VAL

LYS

PRO

HIS

ARG

5

TYR

ARG

PRO

GLY

THR

VAL

ALA

LEU

ARG

GLU

6

ILE

ARG

TYR

GLN

LYS

SER

THR

GLU

LEU

7

LEU

ILE

ARG

LYS

LEU

PRO

PHE

GLN

ARG

LEU

8

VAL

ARG

GLU

ILE

ALA

GLN

ASP

PHE

LYS

THR

9

ASP

LEU

ARG

PHE

GLN

SER

ALA

VAL

MET

10

ALA

LEU

GLN

GLU

ALA

CYS

GLU

ALA

TYR

LEU

11

VAL

GLY

LEU

PHE

GLU

ASP

THR

ASN

LEU

CYS

12

ALA

ILE

HIS

ALA

LYS

ARG

VAL

THR

ILE

MET

13

PRO

LYS

ASP

ILE

GLN

LEU

ALA

ARG

ILE

14

ARG

GLY

GLU

ARG

ALA

Entity 2, nucleosome, H2A 133 residues - Formula weight is not available

1

GLY

PRO

GLY

MET

SER

GLY

ARG

GLY

LYS

GLN

2

GLY

LYS

ALA

ARG

ALA

LYS

ALA

LYS

THR

3

ARG

SER

ARG

ALA

GLY

LEU

GLN

PHE

PRO

4

VAL

GLY

ARG

VAL

HIS

ARG

LEU

ARG

LYS

5

GLY

ASN

TYR

SER

GLU

ARG

VAL

GLY

ALA

GLY

6

ALA

PRO

VAL

TYR

LEU

ALA

VAL

LEU

GLU

7

TYR

LEU

THR

ALA

GLU

ILE

LEU

GLU

LEU

ALA

8

GLY

ASN

ALA

ARG

ASP

ASN

LYS

THR

9

ARG

ILE

PRO

ARG

HIS

LEU

GLN

LEU

ALA

10

ILE

ARG

ASN

ASP

GLU

LEU

ASN

LYS

LEU

11

LEU

GLY

ARG

VAL

THR

ILE

ALA

GLN

GLY

12

VAL

LEU

PRO

ASN

ILE

GLN

ALA

VAL

LEU

13

PRO

LYS

THR

GLU

SER

HIS

LYS

ALA

14

LYS

GLY

LYS

Entity 3, nucleosome, H2B 129 residues - Formula weight is not available

1

GLY

PRO

GLY

MET

PRO

GLU

PRO

ALA

LYS

SER

2

ALA

PRO

ALA

PRO

LYS

GLY

SER

LYS

3

ALA

VAL

THR

LYS

ALA

GLN

LYS

ASP

GLY

4

LYS

ARG

LYS

ARG

SER

ARG

LYS

GLU

SER

5

TYR

SER

ILE

TYR

VAL

TYR

LYS

VAL

LEU

LYS

6

GLN

VAL

HIS

PRO

ASP

THR

GLY

ILE

SER

7

LYS

ALA

MET

GLY

ILE

MET

ASN

SER

PHE

VAL

8

ASN

ASP

ILE

PHE

GLU

ARG

ILE

ALA

GLY

GLU

9

ALA

SER

ARG

LEU

ALA

HIS

TYR

ASN

LYS

ARG

10

SER

THR

ILE

THR

SER

ARG

GLU

ILE

GLN

THR

11

ALA

VAL

ARG

LEU

PRO

GLY

GLU

LEU

12

ALA

LYS

HIS

ALA

VAL

SER

GLU

GLY

THR

LYS

13

ALA

VAL

THR

LYS

TYR

THR

SER

ALA

LYS

Entity 4, nucleosome, H4 102 residues - Formula weight is not available

1

SER

GLY

ARG

GLY

LYS

GLY

LYS

GLY

LEU

2

GLY

LYS

GLY

ALA

LYS

ARG

HIS

ARG

LYS

3

VAL

LEU

ARG

ASP

ASN

ILE

GLN

GLY

ILE

THR

4

LYS

PRO

ALA

ILE

ARG

LEU

ALA

ARG

5

GLY

VAL

LYS

ARG

ILE

SER

GLY

LEU

ILE

6

TYR

GLU

THR

ARG

GLY

VAL

LEU

LYS

VAL

7

PHE

LEU

GLU

ASN

VAL

ILE

ARG

ASP

ALA

VAL

8

THR

TYR

THR

GLU

HIS

ALA

LYS

ARG

LYS

THR

9

VAL

THR

ALA

MET

ASP

VAL

TYR

ALA

LEU

10

LYS

ARG

GLN

GLY

ARG

THR

LEU

TYR

GLY

PHE

11

GLY

Entity 5, DNA 145 residues - Formula weight is not available

1

DA

DT

DC

DA

DG

DA

DT

DC

2

DC

DG

DT

DG

DC

DG

DA

DG

3

DG

DC

DG

DC

DT

DC

DA

DT

4

DT

DG

DT

DC

DG

DT

DA

DG

DA

5

DC

DA

DG

DC

DT

DC

DT

DA

DG

DC

6

DA

DC

DG

DC

DT

DA

7

DC

DG

DC

DA

DC

DG

DT

DA

DC

DG

8

DC

DG

DC

DT

DG

DT

DC

9

DC

DG

DC

DG

DT

DA

10

DC

DG

DC

DA

DG

11

DG

DA

DT

DA

DC

DT

DC

12

DT

DA

DG

DT

DC

DT

DC

DA

DG

13

DG

DC

DA

DC

DG

DT

DG

DT

DC

DA

14

DG

DA

DT

DA

DT

DA

DT

DA

DC

DA

15

DT

DC

DG

DA

DT

Samples:

sample_1: histone H3, [U-100% 13C; U-100% 15N; U-H], 20-260 uM; histone H2A 20-260 uM; histone H2B 20-260 uM; histone H4 20-260 uM; 145-bp DNA 10-130 uM

sample_conditions_1: ionic strength: 25 mM; pH: 6; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 100 mM; pH: 6; pressure: 1 atm; temperature: 293 K

sample_conditions_3: ionic strength: 200 mM; pH: 6; pressure: 1 atm; temperature: 293 K

sample_conditions_4: ionic strength: 300 mM; pH: 6; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_2
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_3
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_4
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_2
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_3
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_4

Software:

Olivia v1.16.x - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III 950 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks