BMRB Entry 17536
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17536
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Title: Molecular Determinants of Paralogue-Specific SUMO-SIM Recognition PubMed: 22147707
Deposition date: 2011-03-20 Original release date: 2011-12-14
Authors: Namanja, Andrew; Li, Yi-Jia; Su, Yang; Wong, Steven; Lu, Jingjun; Colson, Loren; Wu, Chenggang; Li, Shawn; Chen, Yuan
Citation: Namanja, Andrew; Li, Yi-Jia; Su, Yang; Wong, Steven; Lu, Jingjun; Colson, Loren; Wu, Chenggang; Li, Shawn; Chen, Yuan. "Insights into High Affinity Small Ubiquitin-like Modifier (SUMO) Recognition by SUMO-interacting Motifs (SIMs) Revealed by a Combination of NMR and Peptide Array Analysis." J. Biol. Chem. 287, 3231-3240 (2012).
Assembly members:
SUMO1, polymer, 97 residues, 9099.442 Da.
M-IR2_peptide, polymer, 13 residues, 1616.870 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):
SUMO1: MSDQEAKPSTEDLGDKKEGE
YIKLKVIGQDSSEIHFKVKM
TTHLKKLKESYCQRQGVPMN
SLRFLFEGQRIADNHTPKEL
GMEEEDVIEVYQEQTGG
M-IR2_peptide: DNEIEVIIVWEKK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 225 |
| 15N chemical shifts | 92 |
| 1H chemical shifts | 198 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | SUMO1 | 1 |
| 2 | M-IR2 | 2 |
Entities:
Entity 1, SUMO1 97 residues - 9099.442 Da.
| 1 | MET | SER | ASP | GLN | GLU | ALA | LYS | PRO | SER | THR | ||||
| 2 | GLU | ASP | LEU | GLY | ASP | LYS | LYS | GLU | GLY | GLU | ||||
| 3 | TYR | ILE | LYS | LEU | LYS | VAL | ILE | GLY | GLN | ASP | ||||
| 4 | SER | SER | GLU | ILE | HIS | PHE | LYS | VAL | LYS | MET | ||||
| 5 | THR | THR | HIS | LEU | LYS | LYS | LEU | LYS | GLU | SER | ||||
| 6 | TYR | CYS | GLN | ARG | GLN | GLY | VAL | PRO | MET | ASN | ||||
| 7 | SER | LEU | ARG | PHE | LEU | PHE | GLU | GLY | GLN | ARG | ||||
| 8 | ILE | ALA | ASP | ASN | HIS | THR | PRO | LYS | GLU | LEU | ||||
| 9 | GLY | MET | GLU | GLU | GLU | ASP | VAL | ILE | GLU | VAL | ||||
| 10 | TYR | GLN | GLU | GLN | THR | GLY | GLY |
Entity 2, M-IR2 13 residues - 1616.870 Da.
| 1 | ASP | ASN | GLU | ILE | GLU | VAL | ILE | ILE | VAL | TRP | ||||
| 2 | GLU | LYS | LYS |
Samples:
sample_1: SUMO1, [U-13C; U-15N; U-2H], 0.5 mM; M-IR2 peptide 1.0 mM; H2O 90%; D2O 10%
sample_2: SUMO1, [U-15N]; perdeuterated, 0.5 mM; M-IR2 peptide 0.6 mM; H2O 90%; D2O 10%
sample_3: SUMO1, [U-15N; U-2H], 0.6 mM; M-IR2 peptide 0.4 mM; D2O 100%
sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D 15N-edited NOESYHSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC-TOCSY | sample_3 | isotropic | sample_conditions_1 |
Software:
TOPSPIN v2.1, Bruker - collection, processing
SPARKY v3.113, Goddard - chemical shift assignment
HADDOCK v2.0, Bonvin - structure solution
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - analysis, refinement
NMR spectrometers:
- Bruker Avance 600 MHz
Related Database Links:
| BMRB | 16611 25299 |
| PDB | |
| DBJ | BAB22172 BAB27379 BAB93477 BAC40739 BAE35024 |
| EMBL | CAA67898 CAG31129 CAG46944 CAG46953 CAH92616 |
| GB | AAB39999 AAB40388 AAB40390 AAC39959 AAC50733 |
| REF | NP_001005781 NP_001005782 NP_001009672 NP_001030535 NP_001106146 |
| SP | A7WLH8 P63165 P63166 Q2EF74 Q5E9D1 |
| TPG | DAA32560 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts