BMRB Entry 53489
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR53489
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NMR-STAR v3 text file.
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Citation: Paz-Villatoro, Jonathan; Yu, Binhan; Songe, Orion; Wang, Xi; Iwahara, Junji. "Cysteine thiol-to-sulfonate oxidation induces unfolding for the functional switching of the extracellular HMGB1 protein" Proc. Natl. Acad. Sci. U.S.A. 123, e2538042123-e2538042123 (2026).
PubMed: 42133810
Assembly members:
entity_1, polymer, 87 residues, Formula weight is not available
Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli
Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-11
Entity Sequences (FASTA):
entity_1: GDPNAPKRPPSAFFLFXSEY
RPKIKGEHPGLSIGDVAKKL
GEXWNNTAADDKQPYEKKAA
KLKEKYEKDIAAYRAKGKPD
AAKKGVV
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 265 |
| 15N chemical shifts | 85 |
| 1H chemical shifts | 269 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Oxidized HMGB1 B-box domain | 1 |
Entities:
Entity 1, Oxidized HMGB1 B-box domain 87 residues - Formula weight is not available
The first X is cysteine sulfonate (PDB residue code, OCS). The second X is methionine sulfoxide (PDB residue code, SME).
| 1 | GLY | ASP | PRO | ASN | ALA | PRO | LYS | ARG | PRO | PRO | ||||
| 2 | SER | ALA | PHE | PHE | LEU | PHE | OCS | SER | GLU | TYR | ||||
| 3 | ARG | PRO | LYS | ILE | LYS | GLY | GLU | HIS | PRO | GLY | ||||
| 4 | LEU | SER | ILE | GLY | ASP | VAL | ALA | LYS | LYS | LEU | ||||
| 5 | GLY | GLU | SME | TRP | ASN | ASN | THR | ALA | ALA | ASP | ||||
| 6 | ASP | LYS | GLN | PRO | TYR | GLU | LYS | LYS | ALA | ALA | ||||
| 7 | LYS | LEU | LYS | GLU | LYS | TYR | GLU | LYS | ASP | ILE | ||||
| 8 | ALA | ALA | TYR | ARG | ALA | LYS | GLY | LYS | PRO | ASP | ||||
| 9 | ALA | ALA | LYS | LYS | GLY | VAL | VAL |
Samples:
sample_1: potassium phosphate 10 mM; sodium chloride 100 mM; D2O, [U-100% 2H], 5%; HMGB1 B-box domain, [U-99% 13C; U-99% 15N], 0.4 mM
sample_conditions_1: ionic strength: 120 mM; pH: 7.4; pressure: 1 atm; temperature: 308 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HA(CA)NCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HA(CA)CON | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)CBCANCO | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)CBCACON | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)CCCON | sample_1 | isotropic | sample_conditions_1 |
| 2D (HACA)CON | sample_1 | isotropic | sample_conditions_1 |
| 2D (HACA)CON | sample_1 | isotropic | sample_conditions_1 |
| 3D (HA)CACON | sample_1 | isotropic | sample_conditions_1 |
| 3D (HA)CANCO | sample_1 | isotropic | sample_conditions_1 |
| 1D 1H | sample_1 | isotropic | sample_conditions_1 |
| 1D 1H | sample_1 | isotropic | sample_conditions_1 |
Software:
NMRPipe - processing
NMRFAM-SPARKY - data analysis
NMR spectrometers:
- Bruker AVANCE III 600 MHz
- Bruker AVANCE III 750 MHz