BMRB Entry 28042
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR28042
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Title: ubiquitin receptor protein complex PubMed: 32160516
Deposition date: 2019-11-13 Original release date: 2020-03-03
Authors: Lu, Xiuxiu; Walters, Kylie
Citation: Lu, Xiuxiu; Ebelle, Danielle; Matsuo, Hiroshi; Walters, Kylie. "An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure" Structure 28, 495-506.e3 (2020).
Assembly members:
ubiquitin_receptor_A, polymer, 136 residues, Formula weight is not available
ubiquitin_receptor_B, polymer, 36 residues, Formula weight is not available
ubiquitin_receptor_C, polymer, 77 residues, Formula weight is not available
ubiquitin_receptor_D, polymer, 76 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
Entity Sequences (FASTA):
ubiquitin_receptor_A: GPGSMTTSGALFPSLVPGSR
GASNKYLVEFRAGKMSLKGT
TVTPDKRKGLVYIQQTDDSL
IHFCWKDRTSGNVEDDLIIF
PDDCEFKRVPQCPSGRVYVL
KFKAGSKRLFFWMQEPKTDQ
DEEHCRKVNEYLNNPP
ubiquitin_receptor_B: MPGALGASGSSGHELSALGP
GSQEPEPPEPFEYIDD
ubiquitin_receptor_C: MQIFVKTLTGKTITLEVEPS
DTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGD
ubiquitin_receptor_D: MQIFVKTLTGKTITLEVEPS
DTIENVKAKIQDKEGIPPDQ
QRLIFAGRQLEDGRTLSDYN
IQKESTLHLVLRLRGG
| Data type | Count |
| 13C chemical shifts | 1165 |
| 15N chemical shifts | 207 |
| 1H chemical shifts | 1930 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | ubiquitin receptor, chain A | 1 |
| 2 | ubiquitin receptor, chain B | 2 |
| 3 | ubiquitin receptor, chain C | 3 |
| 4 | ubiquitin receptor, chain D | 4 |
Entities:
Entity 1, ubiquitin receptor, chain A 136 residues - Formula weight is not available
| 1 | GLY | PRO | GLY | SER | MET | THR | THR | SER | GLY | ALA | ||||
| 2 | LEU | PHE | PRO | SER | LEU | VAL | PRO | GLY | SER | ARG | ||||
| 3 | GLY | ALA | SER | ASN | LYS | TYR | LEU | VAL | GLU | PHE | ||||
| 4 | ARG | ALA | GLY | LYS | MET | SER | LEU | LYS | GLY | THR | ||||
| 5 | THR | VAL | THR | PRO | ASP | LYS | ARG | LYS | GLY | LEU | ||||
| 6 | VAL | TYR | ILE | GLN | GLN | THR | ASP | ASP | SER | LEU | ||||
| 7 | ILE | HIS | PHE | CYS | TRP | LYS | ASP | ARG | THR | SER | ||||
| 8 | GLY | ASN | VAL | GLU | ASP | ASP | LEU | ILE | ILE | PHE | ||||
| 9 | PRO | ASP | ASP | CYS | GLU | PHE | LYS | ARG | VAL | PRO | ||||
| 10 | GLN | CYS | PRO | SER | GLY | ARG | VAL | TYR | VAL | LEU | ||||
| 11 | LYS | PHE | LYS | ALA | GLY | SER | LYS | ARG | LEU | PHE | ||||
| 12 | PHE | TRP | MET | GLN | GLU | PRO | LYS | THR | ASP | GLN | ||||
| 13 | ASP | GLU | GLU | HIS | CYS | ARG | LYS | VAL | ASN | GLU | ||||
| 14 | TYR | LEU | ASN | ASN | PRO | PRO |
Entity 2, ubiquitin receptor, chain B 36 residues - Formula weight is not available
| 1 | MET | PRO | GLY | ALA | LEU | GLY | ALA | SER | GLY | SER | ||||
| 2 | SER | GLY | HIS | GLU | LEU | SER | ALA | LEU | GLY | PRO | ||||
| 3 | GLY | SER | GLN | GLU | PRO | GLU | PRO | PRO | GLU | PRO | ||||
| 4 | PHE | GLU | TYR | ILE | ASP | ASP |
Entity 3, ubiquitin receptor, chain C 77 residues - Formula weight is not available
| 1 | MET | GLN | ILE | PHE | VAL | LYS | THR | LEU | THR | GLY | ||||
| 2 | LYS | THR | ILE | THR | LEU | GLU | VAL | GLU | PRO | SER | ||||
| 3 | ASP | THR | ILE | GLU | ASN | VAL | LYS | ALA | LYS | ILE | ||||
| 4 | GLN | ASP | LYS | GLU | GLY | ILE | PRO | PRO | ASP | GLN | ||||
| 5 | GLN | ARG | LEU | ILE | PHE | ALA | GLY | LYS | GLN | LEU | ||||
| 6 | GLU | ASP | GLY | ARG | THR | LEU | SER | ASP | TYR | ASN | ||||
| 7 | ILE | GLN | LYS | GLU | SER | THR | LEU | HIS | LEU | VAL | ||||
| 8 | LEU | ARG | LEU | ARG | GLY | GLY | ASP |
Entity 4, ubiquitin receptor, chain D 76 residues - Formula weight is not available
| 1 | MET | GLN | ILE | PHE | VAL | LYS | THR | LEU | THR | GLY | ||||
| 2 | LYS | THR | ILE | THR | LEU | GLU | VAL | GLU | PRO | SER | ||||
| 3 | ASP | THR | ILE | GLU | ASN | VAL | LYS | ALA | LYS | ILE | ||||
| 4 | GLN | ASP | LYS | GLU | GLY | ILE | PRO | PRO | ASP | GLN | ||||
| 5 | GLN | ARG | LEU | ILE | PHE | ALA | GLY | ARG | GLN | LEU | ||||
| 6 | GLU | ASP | GLY | ARG | THR | LEU | SER | ASP | TYR | ASN | ||||
| 7 | ILE | GLN | LYS | GLU | SER | THR | LEU | HIS | LEU | VAL | ||||
| 8 | LEU | ARG | LEU | ARG | GLY | GLY |
Samples:
sample_1: Rpn13, [U-13C], 0.6 mM; Rpn2 0.6 mM; proximal ubiquitin of Diubiquitin, [U-13C], 0.72 mM; proximal ubiquitin of Diubiquitin, [U-13C], 0.72 mM
sample_2: Rpn13, [U-13C], 0.6 mM; Rpn2 0.6 mM; distal ubiquitin of Diubiquitin, [U-13C], 0.72 mM; distal ubiquitin of Diubiquitin, [U-13C], 0.72 mM
sample_conditions_1: ionic strength: 0.11 M; pH: 6.5; pressure: 1 atm; temperature: 298.15 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D half-filtered 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D half-filtered 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
Software:
X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
XEASY, Bartels et al. - data analysis
ProcheckNMR, Laskowski and MacArthur - data analysis
NMR spectrometers:
- Bruker Avance 850 MHz
- Bruker Avance 900 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts