BMRB Entry 19914
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19914
MolProbity Validation Chart
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NMR-STAR v3 text file.
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Title: NMR Structure of KDM5B PHD1 finger in complex with H3K4me0(1-10aa) PubMed: 24952722
Deposition date: 2014-04-16 Original release date: 2014-08-04
Authors: Zhang, Yan; Yang, Huirong; Guo, Xue; Rong, Naiyan; Song, Yujiao; Xu, Youwei; Lan, Wenxian; Xu, Yanhui; Cao, Chunyang
Citation: Zhang, Yan; Yang, Huirong; Guo, Xue; Rong, Naiyan; Rong, Yujiao; Xu, Youwei; Lan, Wenxian; Xu, Yanhui; Cao, Chunyang. "The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B" Protein Cell ., .-. (2014).
Assembly members:
entity_1, polymer, 55 residues, 7360.083 Da.
ZINC ION, non-polymer, 65.409 Da.
entity_3, polymer, 10 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: pGEX-6p-1
Entity Sequences (FASTA):
entity_1: AVDLYVCLLCGSGNDEDRLL
LCDGCDDSYHTFCLIPPLHD
VPKGDWRCPKCLAQE
entity_3: ARTKQTARKS
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 165 |
| 15N chemical shifts | 51 |
| 1H chemical shifts | 396 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | ZINC ION_1 | 2 |
| 3 | ZINC ION_2 | 2 |
| 4 | H3K4me0(1-10aa) | 3 |
Entities:
Entity 1, entity_1 55 residues - 7360.083 Da.
| 1 | ALA | VAL | ASP | LEU | TYR | VAL | CYS | LEU | LEU | CYS | ||||
| 2 | GLY | SER | GLY | ASN | ASP | GLU | ASP | ARG | LEU | LEU | ||||
| 3 | LEU | CYS | ASP | GLY | CYS | ASP | ASP | SER | TYR | HIS | ||||
| 4 | THR | PHE | CYS | LEU | ILE | PRO | PRO | LEU | HIS | ASP | ||||
| 5 | VAL | PRO | LYS | GLY | ASP | TRP | ARG | CYS | PRO | LYS | ||||
| 6 | CYS | LEU | ALA | GLN | GLU |
Entity 2, ZINC ION_1 - Zn - 65.409 Da.
| 1 | ZN |
Entity 3, H3K4me0(1-10aa) 10 residues - Formula weight is not available
| 1 | ALA | ARG | THR | LYS | GLN | THR | ALA | ARG | LYS | SER |
Samples:
sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.8 – 2 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0.1 M; pH: 7.4; pressure: 1 atm; temperature: 293 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
Software:
CNS, Brunger A. T. et.al. - refinement
NMR spectrometers:
- Varian INOVA 600 MHz
Related Database Links:
| BMRB | 19913 |
| PDB | |
| DBJ | BAC30898 BAD90482 BAE37363 BAE89761 BAG53706 |
| EMBL | CAB43532 CAB61368 CAB63108 CAH65222 |
| GB | AAD16061 AAH48180 AAH57318 AAI56050 AAI57032 |
| REF | NP_001026200 NP_001100647 NP_001300971 NP_006609 NP_690855 |
| SP | Q5F3R2 Q80Y84 Q9UGL1 |
| TPG | DAA21261 |
| AlphaFold | Q9UGL1 Q5F3R2 Q80Y84 |
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts