BMRB Entry 15592
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15592
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Title: NMR structure of the ubiquitin associated (UBA) domain of p62 (SQSTM1) in complex with ubiquitin. RDC refined PubMed: 18083707
Deposition date: 2007-12-12 Original release date: 2008-01-16
Authors: Long, Jed; Layfield, Robert; Searle, Mark
Citation: Long, Jed; Gallagher, Thomas; Cavey, James; Sheppard, Paul; Ralston, Stuart; Layfield, Robert; Searle, Mark. "Ubiquitin recognition by the ubiquitin-associated domain of p62 involves a novel conformational switch" J. Biol. Chem. 283, 5427-5440 (2008).
Assembly members:
P62_UBA, polymer, 52 residues, Formula weight is not available
ubiquitin, 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):
P62_UBA: GSPPEADPRLIESLSQMLSM
GFSDEGGWLTRLLQTKNYDI
GAALDTIQYSKH
ubiquitin: MQIFVKTLTGKTITLEVESS
DTIDNVKSKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
- assigned_chemical_shifts
- RDCs
| Data type | Count |
| 13C chemical shifts | 227 |
| 15N chemical shifts | 53 |
| 1H chemical shifts | 339 |
| residual dipolar couplings | 45 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | P62_UBA | 1 |
| 2 | ubiquitin | 2 |
Entities:
Entity 1, P62_UBA 52 residues - Formula weight is not available
P62_UBA
| 1 | GLY | SER | PRO | PRO | GLU | ALA | ASP | PRO | ARG | LEU | ||||
| 2 | ILE | GLU | SER | LEU | SER | GLN | MET | LEU | SER | MET | ||||
| 3 | GLY | PHE | SER | ASP | GLU | GLY | GLY | TRP | LEU | THR | ||||
| 4 | ARG | LEU | LEU | GLN | THR | LYS | ASN | TYR | ASP | ILE | ||||
| 5 | GLY | ALA | ALA | LEU | ASP | THR | ILE | GLN | TYR | SER | ||||
| 6 | LYS | HIS |
Entity 2, ubiquitin 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 | SER | SER | ||||
| 3 | ASP | THR | ILE | ASP | ASN | VAL | LYS | SER | 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 |
Samples:
sample_1: entity, [U-100% 15N], 1 mM; ubiquitin 6 mM; potassium phosphate 50 mM; sodium chloride 50 mM; sodium azide 0.04%; D2O, [U-100% 2H], 10%; H2O 90%
sample_2: entity, [U-100% 13C; U-100% 15N], 1 mM; ubiquitin 6 mM; potassium phosphate 50 mM; sodium chloride 50 mM; sodium azide 0.04%; D2O, [U-100% 2H], 10%; H2O 90%
sample_3: entity, [U-100% 15N], 1 mM; ubiquitin 6 mM; potassium phosphate 50 mM; sodium chloride 50 mM; sodium azide 0.04%; D2O, [U-100% 2H], 10%; H2O 90%
sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC-IPAP | sample_3 | anisotropic | sample_conditions_1 |
Software:
X-PLOR NIH v2.14, Schwieters, Kuszewski, Tjandra and Clore - structure solution
xwinnmr v3.5, Bruker Biospin - collection, processing
CcpNMR v1.0.10, CCPN - chemical shift assignment, data analysis, peak picking
TALOS, Cornilescu, Delaglio and Bax - geometry optimization
NMR spectrometers:
- Bruker Avance 600 MHz
Related Database Links:
| BMRB | 11149 11443 15591 17024 4769 4983 |
| PDB | |
| DBJ | BAC26183 BAG35358 BAG53577 BAG65614 BAI46491 BAA02154 BAA03764 BAA05085 BAA05670 BAA76889 |
| EMBL | CAA69642 CAH90955 CAA07773 CAA10056 CAA11267 CAA11268 CAA21278 |
| GB | AAA93299 AAB02908 AAB17127 AAC50535 AAC52070 AAA03351 AAA19247 AAA32904 AAA32905 AAA32906 |
| REF | NP_001125548 NP_001135770 NP_001135771 NP_001156515 NP_001253287 NP_001031585 NP_001031824 NP_001042915 NP_001045980 NP_001049479 |
| SP | O08623 Q13501 Q5RBA5 Q64337 B9DHA6 P05759 P0C016 P0C224 P0C8R3 |
| TPG | DAA28341 DAA08405 DAA09244 DAA09283 DAA09489 DAA39608 |
| PIR | G85036 JS0657 S28426 S42643 S49332 |
| PRF | 1101405A 1207189A 1515347A 1603402A 1604470A |
| TPD | FAA00316 FAA00317 FAA00318 FAA00319 |
| TPE | CBF76581 CBF85986 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts