BMRB Entry 25230
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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/BMR25230
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Title: Solution Structure of the Human FAAP20 UBZ-Ubiquitin Complex PubMed: 25414354
Deposition date: 2014-09-16 Original release date: 2014-12-01
Authors: Wang, Su; Wojtaszek, Jessica; Zhou, Pei
Citation: Wojtaszek, Jessica; Wang, Su; Kim, Hyungjin; Wu, Qinglin; D'Andrea, Alan; Zhou, Pei. "Ubiquitin recognition by FAAP20 expands the complex interface beyond the canonical UBZ domain" Nucleic Acids Res. 42, 13997-14005 (2014).
Assembly members:
UBZ, polymer, 44 residues, 4853.517 Da.
Ubiquitin, polymer, 78 residues, 8802.141 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):
UBZ: SHMGAAALRSCPMCQKEFAP
RLTQLDVDSHLAQCLAESTE
DVTW
Ubiquitin: SHMQIFVKTLTGKTITLEVE
PSDTIENVKAKIQDKEGIPP
DQQRLIFAGKQLEDGRTLSD
YNIQKESTLHLVLRLRGG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 522 |
| 15N chemical shifts | 122 |
| 1H chemical shifts | 860 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | UBZ | 1 |
| 2 | Ubiquitin | 2 |
| 3 | ZINC ION | 3 |
Entities:
Entity 1, UBZ 44 residues - 4853.517 Da.
Residues 1-3 represent non-native residues leftover after protease cleavage removal of a affinity tag; Residues 4-44 represent the UBZ domain of FAAP20(140-180).
| 1 | SER | HIS | MET | GLY | ALA | ALA | ALA | LEU | ARG | SER | ||||
| 2 | CYS | PRO | MET | CYS | GLN | LYS | GLU | PHE | ALA | PRO | ||||
| 3 | ARG | LEU | THR | GLN | LEU | ASP | VAL | ASP | SER | HIS | ||||
| 4 | LEU | ALA | GLN | CYS | LEU | ALA | GLU | SER | THR | GLU | ||||
| 5 | ASP | VAL | THR | TRP |
Entity 2, Ubiquitin 78 residues - 8802.141 Da.
Residues 1-2 represent non-native residues leftover after protease cleavage removal of an affinity tag; residues 3-78 represent human ubiquitin sequence (1-76).
| 1 | SER | HIS | MET | GLN | ILE | PHE | VAL | LYS | THR | LEU | ||||
| 2 | THR | GLY | LYS | THR | ILE | THR | LEU | GLU | VAL | GLU | ||||
| 3 | PRO | SER | ASP | THR | ILE | GLU | ASN | VAL | LYS | ALA | ||||
| 4 | LYS | ILE | GLN | ASP | LYS | GLU | GLY | ILE | PRO | PRO | ||||
| 5 | ASP | GLN | GLN | ARG | LEU | ILE | PHE | ALA | GLY | LYS | ||||
| 6 | GLN | LEU | GLU | ASP | GLY | ARG | THR | LEU | SER | ASP | ||||
| 7 | TYR | ASN | ILE | GLN | LYS | GLU | SER | THR | LEU | HIS | ||||
| 8 | LEU | VAL | LEU | ARG | LEU | ARG | GLY | GLY |
Entity 3, ZINC ION - Zn - 65.409 Da.
| 1 | ZN |
Samples:
15N13C_Ubi: Ubiquitin, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 25 mM; potassium chloride 100 mM; UBZ 2 mM
15N13C_UBZ_Ubi: UBZ, [U-100% 13C; U-100% 15N], 0.8 mM; Ubiquitin, [U-100% 13C; U-100% 15N], 0.8 mM; sodium phosphate 25 mM; potassium chloride 100 mM
15N13C_UBZ_Ubi_NOE: Ubiquitin, [U-100% 13C; U-100% 15N], 3 mM; sodium phosphate 25 mM; potassium chloride 100 mM; UBZ, [U-100% 13C; U-100% 15N], 3 mM
15N13C_UBZ_NOE: Ubiquitin 3 mM; sodium phosphate 25 mM; potassium chloride 100 mM; UBZ, [U-100% 13C; U-100% 15N], 3 mM
15N13C_Ubi_NOE: Ubiquitin, [U-100% 13C; U-100% 15N], 3 mM; sodium phosphate 25 mM; potassium chloride 100 mM; UBZ 3 mM
15N13C_Ubi_D2O: Ubiquitin, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 25 mM; potassium chloride 100 mM; UBZ 2 mM
15N13C_UBZ_Ubi_D2O: UBZ, [U-100% 13C; U-100% 15N], 0.8 mM; Ubiquitin, [U-100% 13C; U-100% 15N], 0.8 mM; sodium phosphate 25 mM; potassium chloride 100 mM
sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | 15N13C_Ubi | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 4D sparse-sampled HCCH TOCSY | 15N13C_Ubi_D2O | isotropic | sample_conditions_1 |
| 3D sparse-sampled HA(CA)NH | 15N13C_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HNCO | 15N13C_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HNCA | 15N13C_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HNCACB | 15N13C_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HN(CO)CA | 15N13C_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HN(COCA)CB | 15N13C_Ubi | isotropic | sample_conditions_1 |
| 4D sparse-sampled HC(CO)NH-TOCSY | 15N13C_Ubi | isotropic | sample_conditions_1 |
| 4D sparse-sampled CHNH NOESY | 15N13C_Ubi | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | 15N13C_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HA(CACO)NH | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HA(CA)NH | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HNCO | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HNCA | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HNCACB | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HN(CO)CA | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 4D sparse-sampled HC(CO)NH-TOCSY | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 4D sparse-sampled CHNH NOESY | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 3D sparse-sampled HN(COCA)CB | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 4D sparse-sampled CHCH NOESY | 15N13C_UBZ_Ubi_NOE | isotropic | sample_conditions_1 |
| 4D sparse-sampled CHCH NOESY | 15N13C_UBZ_NOE | isotropic | sample_conditions_1 |
| 4D sparse-sampled CHCH NOESY | 15N13C_Ubi_NOE | isotropic | sample_conditions_1 |
| 3D sparse-sampled HNCACO | 15N13C_UBZ_Ubi | isotropic | sample_conditions_1 |
| 4D sparse-sampled HCCH TOCSY | 15N13C_UBZ_Ubi_D2O | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY, Goddard - data analysis
TALOS, Cornilescu, Delaglio and Bax - data analysis
SCRUB, Coggins and Zhou - processing
CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure solution
XEASY, Bartels et al. - data analysis
NMR spectrometers:
- Varian INOVA 600 MHz
- Varian INOVA 800 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts