BMRB Entry 19329
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19329
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Title: Solution NMR Structure of the RING finger domain from the Kip1 ubiquitination-promoting E3 complex protein 1 (KPC1/RNF123) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8700A
Deposition date: 2013-06-28 Original release date: 2013-07-19
Authors: Ramelot, Theresa; Yang, Yunhuang; Janjua, Haleema; Kohan, Eitan; Wang, Huang; Xiao, Rong; Acton, Thomas; Everett, John; Montelione, Gaetano; Kennedy, Michael
Citation: Ramelot, Theresa; Yang, Yunhuang; Janjua, Haleema; Kohan, Eitan; Wang, Huang; Xiao, Rong; Acton, Thomas; Everett, John; Montelione, Gaetano; Kennedy, Michael. "Solution NMR Structure of the RING finger domain from the Kip1 ubiquitination-promoting E3 complex protein 1 (KPC1/RNF123) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8700A" To be published ., .-..
Assembly members:
HR8700A, polymer, 61 residues, 6977.676 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):
HR8700A: SHMPTSEEDLCPICYAHPIS
AVFQPCGHKSCKACINQHLM
NNKDCFFCKTTIVSVEDWEK
G
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 268 |
| 15N chemical shifts | 68 |
| 1H chemical shifts | 409 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | HR8700A | 1 |
| 2 | ZN ion, 1 | 2 |
| 3 | ZN ion, 2 | 2 |
Entities:
Entity 1, HR8700A 61 residues - 6977.676 Da.
First three residues, SHM, are non-native. Residues 1254-1292 of RNF123
| 1 | SER | HIS | MET | PRO | THR | SER | GLU | GLU | ASP | LEU | ||||
| 2 | CYS | PRO | ILE | CYS | TYR | ALA | HIS | PRO | ILE | SER | ||||
| 3 | ALA | VAL | PHE | GLN | PRO | CYS | GLY | HIS | LYS | SER | ||||
| 4 | CYS | LYS | ALA | CYS | ILE | ASN | GLN | HIS | LEU | MET | ||||
| 5 | ASN | ASN | LYS | ASP | CYS | PHE | PHE | CYS | LYS | THR | ||||
| 6 | THR | ILE | VAL | SER | VAL | GLU | ASP | TRP | GLU | LYS | ||||
| 7 | GLY |
Entity 2, ZN ion, 1 - Zn - 65.409 Da.
| 1 | ZN |
Samples:
sample_NC_HR8700A.005: HR8700A.005, [U-15N] 5% 13C-fractional labeling, 1.0 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
sample_D2O_NC_HR8700A.005: HR8700A.005, [U-100% 13C; U-100% 15N], 1.0 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_NC5_HR8700A.007: HR8700A.007, [U-100% 15N] 5% 13C-fractional labeling, 0.9 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
sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic CT | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic noCT | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY NUS | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic NUS | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_D2O_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_NC5_HR8700A.007 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_NC5_HR8700A.007 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC HIS | sample_NC5_HR8700A.007 | isotropic | sample_conditions_1 |
| 1D T1 NSQC array | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 1D T2 NHSQC array | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC NH2 only | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 4D HCCH NOESY | sample_D2O_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D CCH-TOCSY | sample_D2O_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_D2O_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_NC_HR8700A.005 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_NC_HR8700A.005 | 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
AutoStruct v2.1, Huang, Tejero, Powers and Montelione - data analysis,refinement
NMRPipe vNMRPipe-2008, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
TOPSPIN v2.4, Bruker Biospin - collection
VNMRJ vvnmrj_1.1_D, 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 vfmcgui2.5_linux, Alex Lemak, Cheryl Arrowmith - refinement
NMR spectrometers:
- Bruker Avance II 850 MHz
- Varian INOVA 600 MHz
- Bruker Avance III 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts