BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 51140

Title: H3 tail in 193-bp nucleosome   PubMed: 36610636

Deposition date: 2021-10-14 Original release date: 2023-03-10

Authors: Ohtomo, Hideaki

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).

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, 193 residues, Formula weight is not available

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

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

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: ATCGGACCCTATCGCGAGCC AGGCCTGAGAATCCGGTGCC GAGGCCGCTCAATTGGTCGT AGACAGCTCTAGCACCGCTT AAACGCACGTACGCGCTGTC CCCCGCGTTTTAACCGCCAA GGGGATTACTCCCTAGTCTC CAGGCACGTGTCAGATATAT ACATCCAGGCCTTGTGTCGC GAAATTCATAGAT

Data typeCount
15N chemical shifts145
1H chemical shifts145

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1nucleosome, H31
2nucleosome, H2A2
3nucleosome, H2B3
4nucleosome, H44
5DNA5

Entities:

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

1   ALAARGTHRLYSGLNTHRALAARGLYSSER
2   THRGLYGLYLYSALAPROARGLYSGLNLEU
3   ALATHRLYSALAALAARGLYSSERALAPRO
4   ALATHRGLYGLYVALLYSLYSPROHISARG
5   TYRARGPROGLYTHRVALALALEUARGGLU
6   ILEARGARGTYRGLNLYSSERTHRGLULEU
7   LEUILEARGLYSLEUPROPHEGLNARGLEU
8   VALARGGLUILEALAGLNASPPHELYSTHR
9   ASPLEUARGPHEGLNSERSERALAVALMET
10   ALALEUGLNGLUALACYSGLUALATYRLEU
11   VALGLYLEUPHEGLUASPTHRASNLEUCYS
12   ALAILEHISALALYSARGVALTHRILEMET
13   PROLYSASPILEGLNLEUALAARGARGILE
14   ARGGLYGLUARGALA

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

1   GLYPROGLYMETSERGLYARGGLYLYSGLN
2   GLYGLYLYSALAARGALALYSALALYSTHR
3   ARGSERSERARGALAGLYLEUGLNPHEPRO
4   VALGLYARGVALHISARGLEULEUARGLYS
5   GLYASNTYRSERGLUARGVALGLYALAGLY
6   ALAPROVALTYRLEUALAALAVALLEUGLU
7   TYRLEUTHRALAGLUILELEUGLULEUALA
8   GLYASNALAALAARGASPASNLYSLYSTHR
9   ARGILEILEPROARGHISLEUGLNLEUALA
10   ILEARGASNASPGLUGLULEUASNLYSLEU
11   LEUGLYARGVALTHRILEALAGLNGLYGLY
12   VALLEUPROASNILEGLNALAVALLEULEU
13   PROLYSLYSTHRGLUSERHISHISLYSALA
14   LYSGLYLYS

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

1   GLYPROGLYMETPROGLUPROALALYSSER
2   ALAPROALAPROLYSLYSGLYSERLYSLYS
3   ALAVALTHRLYSALAGLNLYSLYSASPGLY
4   LYSLYSARGLYSARGSERARGLYSGLUSER
5   TYRSERILETYRVALTYRLYSVALLEULYS
6   GLNVALHISPROASPTHRGLYILESERSER
7   LYSALAMETGLYILEMETASNSERPHEVAL
8   ASNASPILEPHEGLUARGILEALAGLYGLU
9   ALASERARGLEUALAHISTYRASNLYSARG
10   SERTHRILETHRSERARGGLUILEGLNTHR
11   ALAVALARGLEULEULEUPROGLYGLULEU
12   ALALYSHISALAVALSERGLUGLYTHRLYS
13   ALAVALTHRLYSTYRTHRSERALALYS

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

1   SERGLYARGGLYLYSGLYGLYLYSGLYLEU
2   GLYLYSGLYGLYALALYSARGHISARGLYS
3   VALLEUARGASPASNILEGLNGLYILETHR
4   LYSPROALAILEARGARGLEUALAARGARG
5   GLYGLYVALLYSARGILESERGLYLEUILE
6   TYRGLUGLUTHRARGGLYVALLEULYSVAL
7   PHELEUGLUASNVALILEARGASPALAVAL
8   THRTYRTHRGLUHISALALYSARGLYSTHR
9   VALTHRALAMETASPVALVALTYRALALEU
10   LYSARGGLNGLYARGTHRLEUTYRGLYPHE
11   GLYGLY

Entity 5, DNA 193 residues - Formula weight is not available

1   DADTDCDGDGDADCDCDCDT
2   DADTDCDGDCDGDADGDCDC
3   DADGDGDCDCDTDGDADGDA
4   DADTDCDCDGDGDTDGDCDC
5   DGDADGDGDCDCDGDCDTDC
6   DADADTDTDGDGDTDCDGDT
7   DADGDADCDADGDCDTDCDT
8   DADGDCDADCDCDGDCDTDT
9   DADADADCDGDCDADCDGDT
10   DADCDGDCDGDCDTDGDTDC
11   DCDCDCDCDGDCDGDTDTDT
12   DTDADADCDCDGDCDCDADA
13   DGDGDGDGDADTDTDADCDT
14   DCDCDCDTDADGDTDCDTDC
15   DCDADGDGDCDADCDGDTDG
16   DTDCDADGDADTDADTDADT
17   DADCDADTDCDCDADGDGDC
18   DCDTDTDGDTDGDTDCDGDC
19   DGDADADADTDTDCDADTDA
20   DGDADT

Samples:

sample_1: histone H3, [U-100% 13C; U-100% 15N; U-H], 10-60 uM; histone H2A 10-60 uM; histone H2B 10-60 uM; histone H4 10-60 uM; 193-bp DNA 5-30 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:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
2D 1H-15N TROSYsample_1isotropicsample_conditions_2
2D 1H-15N TROSYsample_1isotropicsample_conditions_3
2D 1H-15N TROSYsample_1isotropicsample_conditions_4
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
2D 1H-15N TROSYsample_1isotropicsample_conditions_2
2D 1H-15N TROSYsample_1isotropicsample_conditions_3
2D 1H-15N TROSYsample_1isotropicsample_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 shifts
SPARKY: Backbone or all simulated shifts