BMRB Entry 16885
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16885
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Title: Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin PubMed: 20929865
Deposition date: 2010-04-20 Original release date: 2010-10-14
Authors: Burschowsky, Daniel; Rudolf, Fabian; Rabut, Gwenael; Herrmann, Torsten; Peter, Matthias; Wider, Gerhard
Citation: Burschowsky, Daniel; Rudolf, Fabian; Rabut, Gwenael; Herrmann, Torsten; Matthias, Peter; Wider, Gerhard. "Structural Analysis of the Conserved Ubiquitin-binding Motifs (UBMs) of the Translesion Polymerase iota in Complex with Ubiquitin." J. Biol. Chem. 286, 1364-1373 (2011).
Assembly members:
DNA_polymerase_iota_UBM1, polymer, 48 residues, 5125.6 Da.
Ubiquitin, polymer, 76 residues, 8576.914 Da.
Natural source: Common Name: House mouse Taxonomy ID: 10013 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
DNA_polymerase_iota_UBM1: GSDTSDLPLQALPEGVDQEV
FKQLPADIQEEILSGKSREN
LKGKGSLS
Ubiquitin: MQIFVKTLTGKTITLEVEPS
DTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 423 |
| 15N chemical shifts | 131 |
| 1H chemical shifts | 909 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | UBM1 | 1 |
| 2 | Ubiquitin | 2 |
Entities:
Entity 1, UBM1 48 residues - 5125.6 Da.
Residues 485-486 represent non-native cloning artifacts. Residues 487-490 and 527-532 represent flexible flanking regions that are not shown in the Structure.
| 1 | GLY | SER | ASP | THR | SER | ASP | LEU | PRO | LEU | GLN | ||||
| 2 | ALA | LEU | PRO | GLU | GLY | VAL | ASP | GLN | GLU | VAL | ||||
| 3 | PHE | LYS | GLN | LEU | PRO | ALA | ASP | ILE | GLN | GLU | ||||
| 4 | GLU | ILE | LEU | SER | GLY | LYS | SER | ARG | GLU | ASN | ||||
| 5 | LEU | LYS | GLY | LYS | GLY | SER | LEU | SER |
Entity 2, Ubiquitin 76 residues - 8576.914 Da.
| 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 |
Samples:
15NUBM1+ub: DNA polymerase iota UBM1, [U-99% 15N], 1 – 2 mM; Ubiquitin4 – 8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; H2O 5%
13C15NUBM1+ub: DNA polymerase iota UBM1, [U-95% 13C; U-99% 15N], 1 – 2 mM; Ubiquitin4 – 8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; H2O 5%
15NUbi+ubm1: DNA polymerase iota UBM11 – 2 mM; Ubiquitin, [U-99% 15N], 4 – 8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; H2O 5%
13C15NUbi+ubm1: DNA polymerase iota UBM11 – 2 mM; Ubiquitin, [U-95% 13C; U-99% 15N], 4 – 8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; H2O 5%
labUbi-overUBM1: DNA polymerase iota UBM11 – 2 mM; Ubiquitin, [U-95% 13C; U-99% 15N], 4 – 8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; H2O 5%
Sample_conditions: ionic strength: 0.189 M; pH: 6.0; pressure: 1 atm; temperature: 288 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCACB | 13C15NUBM1+ub | isotropic | Sample_conditions |
| 3D 1H-15N NOESY | 15NUBM1+ub | isotropic | Sample_conditions |
| 3D 1H-15N TOCSY | 15NUBM1+ub | isotropic | Sample_conditions |
| 3D 1H-13C NOESY | 13C15NUBM1+ub | isotropic | Sample_conditions |
| 3D HCCH-COSY | 13C15NUBM1+ub | isotropic | Sample_conditions |
| 2D 1H-15N HSQC | 15NUBM1+ub | isotropic | Sample_conditions |
| 2D 1H-13C HSQC | 13C15NUBM1+ub | isotropic | Sample_conditions |
| 3D HNCACB | 13C15NUbi+ubm1 | isotropic | Sample_conditions |
| 3D 1H-15N NOESY | 15NUbi+ubm1 | isotropic | Sample_conditions |
| 3D 1H-15N TOCSY | 15NUbi+ubm1 | isotropic | Sample_conditions |
| 3D 1H-13C NOESY | 13C15NUbi+ubm1 | isotropic | Sample_conditions |
| 3D HCCH-COSY | 13C15NUbi+ubm1 | isotropic | Sample_conditions |
| 2D 1H-15N HSQC | 15NUbi+ubm1 | isotropic | Sample_conditions |
| 2D 1H-13C HSQC | 13C15NUbi+ubm1 | isotropic | Sample_conditions |
| 3D 1H-13C-filtered-13C-edited NOESY | 13C15NUBM1+ub | isotropic | Sample_conditions |
| 3D 1H-13C-filtered-13C-edited NOESY | 13C15NUbi+ubm1 | isotropic | Sample_conditions |
| 3D 1H-13C-filtered-13C-edited NOESY | labUbi-overUBM1 | isotropic | Sample_conditions |
Software:
AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement
TOPSPIN v2.1, Bruker Biospin - collection, processing
Molmol v2k.2, Koradi, Billeter and Wuthrich - geometry optimization
UNIO v1.0.4, T. Herrmann - chemical shift assignment, peak picking, structure solution
DYANA, Guntert, Braun and Wuthrich - structure solution
CARA v1.8.4, R. Keller - chemical shift assignment, data analysis
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 750 MHz
- Bruker Avance 900 MHz
Related Database Links:
| PDB | |
| DBJ | BAC25154 BAE26322 BAE32662 BAA03983 BAA09860 BAA11842 BAA11843 BAA23486 |
| GB | AAD50424 AAH82278 AAS75834 AAS75835 AEQ34091 AAA02769 AAA28154 AAA28997 AAA28998 AAA28999 |
| REF | NP_001129562 NP_001276444 NP_001276445 NP_036102 XP_006526008 NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286 |
| SP | Q6R3M4 P0C273 P0C275 P0C276 P0CG47 P0CG48 |
| BMRB | 11505 11547 15047 15410 15689 15866 15907 16228 16582 16626 16763 16880 16895 17059 17181 17239 17333 17439 17769 17919 18582 18583 18584 18610 18611 18737 19394 19399 19406 19412 19447 25070 25230 4245 4375 4983 5101 5387 6457 6466 6470 6488 68 7111 |
| EMBL | CAA25706 CAA26488 CAA28495 CAA30183 CAA30815 |
| PIR | I50437 I51568 I65237 JN0790 S13928 |
| PRF | 0412265A 1101405A 1212243A 1212243B 1212243C |
| TPD | FAA00319 |
| TPG | DAA18802 DAA20663 DAA20672 DAA24675 DAA28295 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts