BMRB Entry 18688
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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/BMR18688
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Title: Backbone amide chemical shifts of gp78 RING bound to Ube2g2:G2BR PubMed: 23942235
Deposition date: 2012-08-30 Original release date: 2013-08-26
Authors: Das, Ranabir; Linag, Yuhe; Mariano, Jennifer; Li, Jess; Huang, Tao; King, Aaren; Weissman, Allan; Ji, Xinhua; Byrd, R. Andrew
Citation: Das, Ranabir; Liang, Yu-He; Mariano, Jennifer; Li, Jess; Huang, Tao; King, Aaren; Tarasov, Sergey; Weissman, Allan; Ji, Xinhua; Byrd, R. Andrew. "Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine." EMBO J. 32, 2504-2516 (2013).
Assembly members:
entity_1, polymer, 156 residues, 17556.293 Da.
entity_2, polymer, 27 residues, 3365.939 Da.
entity_3, polymer, 58 residues, 6473.385 Da.
entity_ZN, non-polymer, 65.409 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: AGTALKRLMAEYKQLTLNPP
EGIVAGPMNEENFFEWEALI
MGPEDTCFEFGVFPAILSFP
LDYPLSPPKMRFTCEMFHPN
IYPDGRVCISILHAPGSAER
WSPVQSVEKILLSVVSMLAE
PNDESGANVDASKMWRDDRE
QFYKIAKQIVQKSLGL
entity_2: SADERQRMLVQRKDELLQQA
RKRFLNK
entity_3: AVATPEELAVNNDDCAICWD
SMQAARKLPCGHLFHNSCLR
SWLEQDTSCPTCRMSLNI
- assigned_chemical_shifts
| Data type | Count |
| 15N chemical shifts | 55 |
| 1H chemical shifts | 55 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
| 3 | entity_3 | 3 |
| 4 | ZINC ION_1 | 4 |
| 5 | ZINC ION_2 | 4 |
Entities:
Entity 1, entity_1 156 residues - 17556.293 Da.
| 1 | ALA | GLY | THR | ALA | LEU | LYS | ARG | LEU | MET | ALA | ||||
| 2 | GLU | TYR | LYS | GLN | LEU | THR | LEU | ASN | PRO | PRO | ||||
| 3 | GLU | GLY | ILE | VAL | ALA | GLY | PRO | MET | ASN | GLU | ||||
| 4 | GLU | ASN | PHE | PHE | GLU | TRP | GLU | ALA | LEU | ILE | ||||
| 5 | MET | GLY | PRO | GLU | ASP | THR | CYS | PHE | GLU | PHE | ||||
| 6 | GLY | VAL | PHE | PRO | ALA | ILE | LEU | SER | PHE | PRO | ||||
| 7 | LEU | ASP | TYR | PRO | LEU | SER | PRO | PRO | LYS | MET | ||||
| 8 | ARG | PHE | THR | CYS | GLU | MET | PHE | HIS | PRO | ASN | ||||
| 9 | ILE | TYR | PRO | ASP | GLY | ARG | VAL | CYS | ILE | SER | ||||
| 10 | ILE | LEU | HIS | ALA | PRO | GLY | SER | ALA | GLU | ARG | ||||
| 11 | TRP | SER | PRO | VAL | GLN | SER | VAL | GLU | LYS | ILE | ||||
| 12 | LEU | LEU | SER | VAL | VAL | SER | MET | LEU | ALA | GLU | ||||
| 13 | PRO | ASN | ASP | GLU | SER | GLY | ALA | ASN | VAL | ASP | ||||
| 14 | ALA | SER | LYS | MET | TRP | ARG | ASP | ASP | ARG | GLU | ||||
| 15 | GLN | PHE | TYR | LYS | ILE | ALA | LYS | GLN | ILE | VAL | ||||
| 16 | GLN | LYS | SER | LEU | GLY | LEU |
Entity 2, entity_2 27 residues - 3365.939 Da.
| 1 | SER | ALA | ASP | GLU | ARG | GLN | ARG | MET | LEU | VAL | ||||
| 2 | GLN | ARG | LYS | ASP | GLU | LEU | LEU | GLN | GLN | ALA | ||||
| 3 | ARG | LYS | ARG | PHE | LEU | ASN | LYS |
Entity 3, entity_3 58 residues - 6473.385 Da.
| 1 | ALA | VAL | ALA | THR | PRO | GLU | GLU | LEU | ALA | VAL | ||||
| 2 | ASN | ASN | ASP | ASP | CYS | ALA | ILE | CYS | TRP | ASP | ||||
| 3 | SER | MET | GLN | ALA | ALA | ARG | LYS | LEU | PRO | CYS | ||||
| 4 | GLY | HIS | LEU | PHE | HIS | ASN | SER | CYS | LEU | ARG | ||||
| 5 | SER | TRP | LEU | GLU | GLN | ASP | THR | SER | CYS | PRO | ||||
| 6 | THR | CYS | ARG | MET | SER | LEU | ASN | ILE |
Entity 4, ZINC ION_1 - Zn - 65.409 Da.
| 1 | ZN |
Samples:
sample_1: gp78RING, [U-100% 13C; U-100% 15N], 0.7 – 1 mM; TRIS 50 mM; TCEP 2 mM; sodium azide 0.2 mM
sample_conditions_1: ionic strength: 0 M; pH: 7.2; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
Software:
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution
SPARKY, Goddard - chemical shift assignment, data analysis
NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
CNS, Alexandre Bonvin - structure solution
NMR spectrometers:
- Varian INOVA 600 MHz
- Varian INOVA 500 MHz
Related Database Links:
| REF | XP_007486190 NP_001135 NP_001267243 XP_001091030 XP_002761010 XP_003263117 NP_001039439 NP_001135 NP_001267243 NP_001271666 NP_035917 |
| PDB | |
| DBJ | BAE01277 BAK63135 BAE01277 BAE34049 BAE41974 BAE87377 BAK63135 |
| GB | AAA36671 AAA79362 AAD56722 AAH17043 AAH56869 AAD56721 AAD56722 AAH17043 AAH34538 AAH40338 |
| SP | Q9UKV5 Q9R049 Q9UKV5 |
| BMRB | 18677 |
| TPG | DAA20037 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts