BMRB Entry 51820
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51820
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Title: 13C,15N solid-state NMR assignments of H2B globular domain in NCP PubMed: 37355718
Deposition date: 2023-02-03 Original release date: 2023-06-26
Authors: Shi, Xiangyan
Citation: Shi, Xiangyan; Kannaian, Bhuvaneswari; Prasanna, Chinmayi; Soman, Aghil; Nordenskiold, Lars. "Structural and dynamical investigation of histone H2B in well-hydrated nucleosome core particles by solid-state NMR" Commun. Biol. 6, 672-672 (2023).
Assembly members:
entity_1, polymer, 122 residues, Formula weight is not available
entity_2, polymer, 129 residues, Formula weight is not available
entity_3, polymer, 135 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
entity_6, polymer, 145 residues, Formula weight is not available
Natural source: Common Name: African clawed frog Taxonomy ID: 8355 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Xenopus laevis
Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-3a
Entity Sequences (FASTA):
entity_1: AKSAPAPKKGSKKAVTKAQK
KDGKKRRKTRKESYAIYVYK
VLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHY
NKRSTITSREIQTAVRLLLP
GELAKHAVSEGTKAVTKYTS
AK
entity_2: SGRGKQGGKARAKAKTRSSR
AGLQFPVGRVHRLLRKGNYS
ERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIP
RHLQLAIRNDEELNKLLGRV
TIAQGGVLPNIQAVLLPKKT
ESHHKAKGK
entity_3: ARTKQTARKSTGGKAPRKQL
ATKAARKSAPATGGVKKPHR
YRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKT
DLRFQSSAVMALQEACEAYL
VGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
entity_4: SGRGKGGKGLGKGGAKRHRK
VLRDNIQGITKPAIRRLARR
GGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKT
VTAMDVVYALKRQGRTLYGF
GG
entity_5: ATCAGAATCCCGGTGCCGAG
GCCGCTCAATTGGTCGTAGA
CAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCC
CGCGTTTTAACCGCCAAGGG
GATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACA
TCGAT
entity_6: ATCGATGTATATATCTGACA
CGTGCCTGGAGACTAGGGAG
TAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTAC
GTGCGTTTAAGCGGTGCTAG
AGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATT
CTGAT
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 380 |
| 15N chemical shifts | 93 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | H2B | 1 |
| 2 | H2A | 2 |
| 3 | H3 | 3 |
| 4 | H4 | 4 |
| 5 | DNA 1 | 5 |
| 6 | DNA 2 | 6 |
Entities:
Entity 1, H2B 122 residues - Formula weight is not available
| 1 | ALA | LYS | SER | ALA | PRO | ALA | PRO | LYS | LYS | GLY | ||||
| 2 | SER | LYS | LYS | ALA | VAL | THR | LYS | ALA | GLN | LYS | ||||
| 3 | LYS | ASP | GLY | LYS | LYS | ARG | ARG | LYS | THR | ARG | ||||
| 4 | LYS | GLU | SER | TYR | ALA | ILE | TYR | VAL | TYR | LYS | ||||
| 5 | VAL | LEU | LYS | GLN | VAL | HIS | PRO | ASP | THR | GLY | ||||
| 6 | ILE | SER | SER | LYS | ALA | MET | SER | ILE | MET | ASN | ||||
| 7 | SER | PHE | VAL | ASN | ASP | VAL | PHE | GLU | ARG | ILE | ||||
| 8 | ALA | GLY | GLU | ALA | SER | ARG | LEU | ALA | HIS | TYR | ||||
| 9 | ASN | LYS | ARG | SER | THR | ILE | THR | SER | ARG | GLU | ||||
| 10 | ILE | GLN | THR | ALA | VAL | ARG | LEU | LEU | LEU | PRO | ||||
| 11 | GLY | GLU | LEU | ALA | LYS | HIS | ALA | VAL | SER | GLU | ||||
| 12 | GLY | THR | LYS | ALA | VAL | THR | LYS | TYR | THR | SER | ||||
| 13 | ALA | LYS |
Entity 2, H2A 129 residues - Formula weight is not available
| 1 | SER | GLY | ARG | GLY | LYS | GLN | GLY | GLY | LYS | ALA | ||||
| 2 | ARG | ALA | LYS | ALA | LYS | THR | ARG | SER | SER | ARG | ||||
| 3 | ALA | GLY | LEU | GLN | PHE | PRO | VAL | GLY | ARG | VAL | ||||
| 4 | HIS | ARG | LEU | LEU | ARG | LYS | GLY | ASN | TYR | SER | ||||
| 5 | GLU | ARG | VAL | GLY | ALA | GLY | ALA | PRO | VAL | TYR | ||||
| 6 | LEU | ALA | ALA | VAL | LEU | GLU | TYR | LEU | THR | ALA | ||||
| 7 | GLU | ILE | LEU | GLU | LEU | ALA | GLY | ASN | ALA | ALA | ||||
| 8 | ARG | ASP | ASN | LYS | LYS | THR | ARG | ILE | ILE | PRO | ||||
| 9 | ARG | HIS | LEU | GLN | LEU | ALA | ILE | ARG | ASN | ASP | ||||
| 10 | GLU | GLU | LEU | ASN | LYS | LEU | LEU | GLY | ARG | VAL | ||||
| 11 | THR | ILE | ALA | GLN | GLY | GLY | VAL | LEU | PRO | ASN | ||||
| 12 | ILE | GLN | ALA | VAL | LEU | LEU | PRO | LYS | LYS | THR | ||||
| 13 | GLU | SER | HIS | HIS | LYS | ALA | LYS | GLY | LYS |
Entity 3, H3 135 residues - Formula weight is not available
| 1 | ALA | ARG | THR | LYS | GLN | THR | ALA | ARG | LYS | SER | ||||
| 2 | THR | GLY | GLY | LYS | ALA | PRO | ARG | LYS | GLN | LEU | ||||
| 3 | ALA | THR | LYS | ALA | ALA | ARG | LYS | SER | ALA | PRO | ||||
| 4 | ALA | THR | GLY | GLY | VAL | LYS | LYS | PRO | HIS | ARG | ||||
| 5 | TYR | ARG | PRO | GLY | THR | VAL | ALA | LEU | ARG | GLU | ||||
| 6 | ILE | ARG | 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 | 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 | ARG | ILE | ||||
| 14 | ARG | GLY | GLU | ARG | ALA |
Entity 4, H4 102 residues - Formula weight is not available
| 1 | SER | GLY | ARG | GLY | LYS | GLY | GLY | LYS | GLY | LEU | ||||
| 2 | GLY | LYS | GLY | GLY | ALA | LYS | ARG | HIS | ARG | LYS | ||||
| 3 | VAL | LEU | ARG | ASP | ASN | ILE | GLN | GLY | ILE | THR | ||||
| 4 | LYS | PRO | ALA | ILE | ARG | ARG | LEU | ALA | ARG | ARG | ||||
| 5 | GLY | GLY | VAL | LYS | ARG | ILE | SER | GLY | LEU | ILE | ||||
| 6 | TYR | GLU | 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 | VAL | TYR | ALA | LEU | ||||
| 10 | LYS | ARG | GLN | GLY | ARG | THR | LEU | TYR | GLY | PHE | ||||
| 11 | GLY | GLY |
Entity 5, DNA 1 145 residues - Formula weight is not available
| 1 | DA | DT | DC | DA | DG | DA | DA | DT | DC | DC | ||||
| 2 | DC | DG | DG | DT | DG | DC | DC | DG | DA | DG | ||||
| 3 | DG | DC | DC | DG | DC | DT | DC | DA | DA | DT | ||||
| 4 | DT | DG | DG | DT | DC | DG | DT | DA | DG | DA | ||||
| 5 | DC | DA | DG | DC | DT | DC | DT | DA | DG | DC | ||||
| 6 | DA | DC | DC | DG | DC | DT | DT | DA | DA | DA | ||||
| 7 | DC | DG | DC | DA | DC | DG | DT | DA | DC | DG | ||||
| 8 | DC | DG | DC | DT | DG | DT | DC | DC | DC | DC | ||||
| 9 | DC | DG | DC | DG | DT | DT | DT | DT | DA | DA | ||||
| 10 | DC | DC | DG | DC | DC | DA | DA | DG | DG | DG | ||||
| 11 | DG | DA | DT | DT | DA | DC | DT | DC | DC | DC | ||||
| 12 | DT | DA | DG | DT | DC | DT | DC | 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 |
Entity 6, DNA 2 145 residues - Formula weight is not available
| 1 | DA | DT | DC | DG | DA | DT | DG | DT | DA | DT | ||||
| 2 | DA | DT | DA | DT | DC | DT | DG | DA | DC | DA | ||||
| 3 | DC | DG | DT | DG | DC | DC | DT | DG | DG | DA | ||||
| 4 | DG | DA | DC | DT | DA | DG | DG | DG | DA | DG | ||||
| 5 | DT | DA | DA | DT | DC | DC | DC | DC | DT | DT | ||||
| 6 | DG | DG | DC | DG | DG | DT | DT | DA | DA | DA | ||||
| 7 | DA | DC | DG | DC | DG | DG | DG | DG | DG | DA | ||||
| 8 | DC | DA | DG | DC | DG | DC | DG | DT | DA | DC | ||||
| 9 | DG | DT | DG | DC | DG | DT | DT | DT | DA | DA | ||||
| 10 | DG | DC | DG | DG | DT | DG | DC | DT | DA | DG | ||||
| 11 | DA | DG | DC | DT | DG | DT | DC | DT | DA | DC | ||||
| 12 | DG | DA | DC | DC | DA | DA | DT | DT | DG | DA | ||||
| 13 | DG | DC | DG | DG | DC | DC | DT | DC | DG | DG | ||||
| 14 | DC | DA | DC | DC | DG | DG | DG | DA | DT | DT | ||||
| 15 | DC | DT | DG | DA | DT |
Samples:
sample_1: NCP(13C, 15N labeled H2B ), [U-98% 13C; U-98% 15N], 33 % w/w
sample_conditions_1: temperature: 285 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D DARR | sample_1 | isotropic | sample_conditions_1 |
| 2D NCA | sample_1 | isotropic | sample_conditions_1 |
| 2D NCO | sample_1 | isotropic | sample_conditions_1 |
| 3D CANCO | sample_1 | isotropic | sample_conditions_1 |
| 3D NCACX | sample_1 | isotropic | sample_conditions_1 |
| 3D NCOCX | sample_1 | isotropic | sample_conditions_1 |
| 1D 1H-13C CP | sample_1 | isotropic | sample_conditions_1 |
| 2D CC DREAM | sample_1 | isotropic | sample_conditions_1 |
Software:
SPARKY - chemical shift assignment
NMRPipe - data analysis
TOPSPIN - collection
NMR spectrometers:
- Bruker AVANCE III 800 MHz