BMRB Entry 19961
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR19961
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Title: Solution structure of SUMO Dimer in Complex with SIM2-3 from RNF4 PubMed: 24969970
Deposition date: 2014-05-09 Original release date: 2014-06-30
Authors: Xu, Yingqi; Plechanovov, Anna; Simpson, Pete; Marchant, Jan; Leidecker, Orsolya; Sebastian, Kraatz; Hay, Ronald; Matthews, Stephen
Citation: Xu, Yingqi; Plechanovov, Anna; Simpson, Pete; Marchant, Jan; Leidecker, Orsolya; Sebastian, Kraatz; Hay, Ronald; Matthews, Stephen. "Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4" Nat. Commun. 5, 4217-4217 (2014).
Assembly members:
entity_1, polymer, 82 residues, 9350.515 Da.
entity_2, polymer, 90 residues, 10351.681 Da.
entity_3, polymer, 25 residues, 2713.963 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):
entity_1: GTENDHINLKVAGQDGSVVQ
FKIKRHTPLSKLMKAYCERQ
GLSMRQIRFRFDGQPINETD
TPAQLEMEDEDTIDVFQQQT
GG
entity_2: GSEEKPKEGVKTENDHINLK
VAGQDGSVVQFKIKRHTPLS
KLMKAYCERQGLSMRQIRFR
FDGQPINETDTPAQLEMEDE
DTIDVFQQQT
entity_3: TVGDEIVDLTCESLEPVVVD
LTHND
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 484 |
| 1H chemical shifts | 919 |
| 15N chemical shifts | 113 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
| 3 | entity_3 | 3 |
Entities:
Entity 1, entity_1 82 residues - 9350.515 Da.
| 1 | GLY | THR | GLU | ASN | ASP | HIS | ILE | ASN | LEU | LYS | ||||
| 2 | VAL | ALA | GLY | GLN | ASP | GLY | SER | VAL | VAL | GLN | ||||
| 3 | PHE | LYS | ILE | LYS | ARG | HIS | THR | PRO | LEU | SER | ||||
| 4 | LYS | LEU | MET | LYS | ALA | TYR | CYS | GLU | ARG | GLN | ||||
| 5 | GLY | LEU | SER | MET | ARG | GLN | ILE | ARG | PHE | ARG | ||||
| 6 | PHE | ASP | GLY | GLN | PRO | ILE | ASN | GLU | THR | ASP | ||||
| 7 | THR | PRO | ALA | GLN | LEU | GLU | MET | GLU | ASP | GLU | ||||
| 8 | ASP | THR | ILE | ASP | VAL | PHE | GLN | GLN | GLN | THR | ||||
| 9 | GLY | GLY |
Entity 2, entity_2 90 residues - 10351.681 Da.
| 1 | GLY | SER | GLU | GLU | LYS | PRO | LYS | GLU | GLY | VAL | |
| 2 | LYS | THR | GLU | ASN | ASP | HIS | ILE | ASN | LEU | LYS | |
| 3 | VAL | ALA | GLY | GLN | ASP | GLY | SER | VAL | VAL | GLN | |
| 4 | PHE | LYS | ILE | LYS | ARG | HIS | THR | PRO | LEU | SER | |
| 5 | LYS | LEU | MET | LYS | ALA | TYR | CYS | GLU | ARG | GLN | |
| 6 | GLY | LEU | SER | MET | ARG | GLN | ILE | ARG | PHE | ARG | |
| 7 | PHE | ASP | GLY | GLN | PRO | ILE | ASN | GLU | THR | ASP | |
| 8 | THR | PRO | ALA | GLN | LEU | GLU | MET | GLU | ASP | GLU | |
| 9 | ASP | THR | ILE | ASP | VAL | PHE | GLN | GLN | GLN | THR |
Entity 3, entity_3 25 residues - 2713.963 Da.
| 1 | THR | VAL | GLY | ASP | GLU | ILE | VAL | ASP | LEU | THR | ||||
| 2 | CYS | GLU | SER | LEU | GLU | PRO | VAL | VAL | VAL | ASP | ||||
| 3 | LEU | THR | HIS | ASN | ASP |
Samples:
sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.3 mM; entity_2 0.3 mM; entity_3 1.0 mM
sample_2: entity_1 0.3 mM; entity_2, [U-99% 13C; U-99% 15N], 0.3 mM; entity_3 1.0 mM
sample_3: entity_1, [U-99% 13C; U-99% 15N], 0.3 mM; entity_2 0.3 mM
sample_4: entity_1 0.3 mM; entity_2, [U-99% 13C; U-99% 15N], 0.3 mM
sample_conditions_1: temperature: 303 K; pH: 7.0; pressure: 1 atm; ionic strength: 0.1 M
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_4 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_3 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_3 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_3 | isotropic | sample_conditions_1 |
Software:
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution
ARIA, Linge, O, . - structure solution
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView, Johnson, One Moon Scientific - chemical shift assignment
TOPSPIN, Bruker Biospin - collection
NMR spectrometers:
- Bruker DRX 600 MHz
Related Database Links:
| BMRB | 11267 |
| PDB | |
| DBJ | BAB28360 BAB28442 BAB28601 BAC39397 BAD96311 BAB28442 BAB28601 BAD96311 BAE28469 BAE29276 BAB31585 BAC41119 BAE26531 BAE27641 BAE30125 |
| EMBL | CAA67896 CAA67897 CAG10356 CAG32064 CAG32742 CAA67896 CAG32742 CAG46970 CAG46985 CAJ81372 |
| GB | AAB49682 AAB92355 AAC99333 AAD45399 AAH00036 AAC99333 AAH00036 AAH08420 AAH54172 AAH58303 AAC35248 AAC53539 AAF00620 AAH03282 AAH62024 |
| REF | NP_001002677 NP_001003422 NP_001004853 NP_001016406 NP_001019466 NP_001002677 NP_001004853 NP_001019466 NP_001069917 NP_001072966 NP_001291198 NP_001291199 NP_035408 NP_062055 XP_006503868 |
| SP | P55854 P61955 P61956 P61957 P61958 P55854 Q17QV3 Q5XIF4 Q5ZHQ1 Q6DI05 O88846 Q9QZS2 |
| TPG | DAA13334 DAA18189 DAA33002 DAA22297 DAA33002 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts