BMRB Entry 19328
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19328
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Title: Solution NMR structure of PHD type Zinc finger domain of Lysine-specific demethylase 5B (PLU-1/JARID1B) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7375C
Deposition date: 2013-06-28 Original release date: 2013-08-02
Authors: Hassan, Faizule; Ramelot, Theresa; Yang, Yunhuang; Cort, John; Janjua, Haleema; Kohan, Eitan; Lee, Dan; Xiao, Rong; Acton, Thomas; Everett, John; Montelione, Gaetano; Kennedy, Michael
Citation: Hassan, Faizule; Ramelot, Theresa; Yang, Yunhuang; Cort, John; Janjua, Haleema; Kohan, Eitan; Lee, Dan; Xiao, Rong; Acton, Thomas; Everett, John; Montelione, Gaetano; Kennedy, Michael. "Solution NMR structure of PHD type Zinc finger domain of Lysine-specific demethylase 5B (PLU-1/JARID1B) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7375C" To be published ., .-..
Assembly members:
HR7375C, polymer, 61 residues, 6934.479 Da.
entity_ZN, non-polymer, 65.409 Da.
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
Entity Sequences (FASTA):
HR7375C: SHMCPAVSCLQPEGDEVDWV
QCDGSCNQWFHQVCVGVSPE
MAEKEDYICVRCTVKDAPSR
K
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 1H chemical shifts | 390 |
| 13C chemical shifts | 251 |
| 15N chemical shifts | 62 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | HR7375C | 1 |
| 2 | Zinc ion, 1 | 2 |
| 3 | Zinc ion, 2 | 2 |
Entities:
Entity 1, HR7375C 61 residues - 6934.479 Da.
Three non-native residues at the N-terminus, SHM. Residues 1487 to 1544 from KDM5B.
| 1 | SER | HIS | MET | CYS | PRO | ALA | VAL | SER | CYS | LEU | ||||
| 2 | GLN | PRO | GLU | GLY | ASP | GLU | VAL | ASP | TRP | VAL | ||||
| 3 | GLN | CYS | ASP | GLY | SER | CYS | ASN | GLN | TRP | PHE | ||||
| 4 | HIS | GLN | VAL | CYS | VAL | GLY | VAL | SER | PRO | GLU | ||||
| 5 | MET | ALA | GLU | LYS | GLU | ASP | TYR | ILE | CYS | VAL | ||||
| 6 | ARG | CYS | THR | VAL | LYS | ASP | ALA | PRO | SER | ARG | ||||
| 7 | LYS |
Entity 2, Zinc ion, 1 - Zn - 65.409 Da.
| 1 | ZN |
Samples:
NC_HR7375C.005: HR7375C.005, [U-100% 13C; U-100% 15N], 1.04 mM; NaN3 0.02%; DTT 10 mM; CaCL2 5 mM; NaCL 100 mM; Proteinase Inhibitors 1 x; MES pH 6.5 20 mM; D2O 10%; DSS 50 uM
NC_HR7375C.006: HR7375C.006, [U-100% 13C; U-100% 15N], 1.04 mM; NaN3 0.02%; DTT 10 mM; CaCL2 5 mM; NaCL 100 mM; Proteinase Inhibitors 1 x; MES pH 6.5 20 mM; D2O 10%; DSS 50 uM
NC5_HR7375C.007: HR7375C.007, [U-100% 15N] 5% 13C fractionally labeled, 0.33 mM; NaN3 0.02%; DTT 10 mM; CaCL2 5 mM; NaCL 100 mM; Proteinase Inhibitors 1 x; MES pH 6.5 20 mM; D2O 10%; DSS 50 uM
D2O_NC_HR7375C.005: HR7375C.005, [U-100% 13C; U-100% 15N], 1.04 mM; NaN3 0.02%; DTT 10 mM; CaCL2 5 mM; NaCL 100 mM; Proteinase Inhibitors 1 x; MES pH 6.5 20 mM; D2O 100%; DSS 50 uM
sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY NUS | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic NUS | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic NUS | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | NC5_HR7375C.007 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | NC5_HR7375C.007 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC HIS | NC5_HR7375C.007 | isotropic | sample_conditions_1 |
| 1D 1H-15N HSQC T1 array | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 1D 1H-15N HSQC T2 array | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC NH2 only | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic ct | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic noct | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D HNCACB | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D HNCO | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D CCH-TOCSY | NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | D2O_NC_HR7375C.005 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | NC_HR7375C.006 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | NC_HR7375C.006 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | NC_HR7375C.006 | isotropic | sample_conditions_1 |
Software:
CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinemen,structure solution,geometry optimization
CYANA v3.0, Guntert, Mumenthaler and Wuthrich - refinement,geometry optimization,structure solution
AutoStructure v2.1, Huang, Tejero, Powers and Montelione - data analysis,refinement
NMRPipe vNMRPipe-2008//nmrbin.linux9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
TOPSPIN v2.4, Bruker Biospin - collection
VNMRJ, Varian - collection
PINE, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment
SPARKY v3.113, Goddard - data analysis
TALOS+ vVersion 1.2009.0721.18, Shen, Cornilescu, Delaglio and Bax - geometry optimization
PSVS v1.4, Bhattacharya, Montelione - structure validation
FMCGUI vfmcgui2.1_linux, Alex Lemak, Cheryl Arrowmith - refinement
NMR spectrometers:
- Bruker Avance II 850 MHz
- Varian INOVA 600 MHz
- Varian INOVA 750 MHz
Related Database Links:
| UNP | Q9UGL1 |
| HUGO | KD5MB |
| PDB | |
| DBJ | BAG51084 |
| EMBL | CAB43532 CAB61368 CAB61375 CAB61395 CAB63108 |
| GB | AAD16061 AAI56050 AAI57032 EAW91433 EAW91435 |
| REF | NP_001300971 NP_006609 XP_002807770 XP_002808303 XP_003792395 |
| SP | Q9UGL1 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts