BMRB Entry 19837
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19837
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Title: NMR structure of E. coli Trigger Factor in complex with unfolded PhoA365-471 PubMed: 24812405
Deposition date: 2014-03-05 Original release date: 2014-05-20
Authors: Saio, Tomohide; Guan, Xiao; Rossi, Paolo; Economou, Anastassios; Kalodimos, Charalampos
Citation: Saio, Tomohide; Guan, Xiao; Rossi, Paolo; Economou, Anastassios; Kalodimos, Charalampos. "Structural basis for protein antiaggregation activity of the trigger factor chaperone" Science 344, 1250494-1250494 (2014).
Assembly members:
entity_1, polymer, 114 residues, 11880.312 Da.
entity_2, polymer, 443 residues, 48256.020 Da.
Natural source: Common Name: E. coli Taxonomy ID: 469008 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: HMQIGETVDLDEAVQRALEF
AKKEGNTLVIVTADHAHASQ
IVAPDTKAPGLTQALNTKDG
AVMVMSYGNSEEDSQEHTGS
QLRIAAYGPHAANVVGLTDQ
TDLFYTMKAALGLK
entity_2: MNHKVHHHHHHMQVSVETTQ
GLGRRVTITIAADSIETAVK
SELVNVAKKVRIDGFRKGKV
PMNIVAQRYGASVRQDVLGD
LMSRNFIDAIIKEKINPAGA
PTYVPGEYKLGEDFTYSVEF
EVYPEVELQGLEAIEVEKPI
VEVTDADVDGMLDTLRKQQA
TWKEKDGAVEAEDRVTIDFT
GSVDGEEFEGGKASDFVLAM
GQGRMIPGFEDGIKGHKAGE
EFTIDVTFPEEYHAENLKGK
AAKFAINLKKVEERELPELT
AEFIKRFGVEDGSVEGLRAE
VRKNMERELKSAIRNRVKSQ
AIEGLVKANDIDVPAALIDS
EIDVLRRQAAQRFGGNEKQA
LELPRELFEEQAKRRVVVGL
LLGEVIRTNELKADEERVKG
LIEEMASAYEDPKEVIEFYS
KNKELMDNMRNVALEEQAVE
AVLAKAKVTEKETTFNELMN
QQA
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 445 |
| 15N chemical shifts | 345 |
| 1H chemical shifts | 1306 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
Entities:
Entity 1, entity_1 114 residues - 11880.312 Da.
| 1 | HIS | MET | GLN | ILE | GLY | GLU | THR | VAL | ASP | LEU | ||||
| 2 | ASP | GLU | ALA | VAL | GLN | ARG | ALA | LEU | GLU | PHE | ||||
| 3 | ALA | LYS | LYS | GLU | GLY | ASN | THR | LEU | VAL | ILE | ||||
| 4 | VAL | THR | ALA | ASP | HIS | ALA | HIS | ALA | SER | GLN | ||||
| 5 | ILE | VAL | ALA | PRO | ASP | THR | LYS | ALA | PRO | GLY | ||||
| 6 | LEU | THR | GLN | ALA | LEU | ASN | THR | LYS | ASP | GLY | ||||
| 7 | ALA | VAL | MET | VAL | MET | SER | TYR | GLY | ASN | SER | ||||
| 8 | GLU | GLU | ASP | SER | GLN | GLU | HIS | THR | GLY | SER | ||||
| 9 | GLN | LEU | ARG | ILE | ALA | ALA | TYR | GLY | PRO | HIS | ||||
| 10 | ALA | ALA | ASN | VAL | VAL | GLY | LEU | THR | ASP | GLN | ||||
| 11 | THR | ASP | LEU | PHE | TYR | THR | MET | LYS | ALA | ALA | ||||
| 12 | LEU | GLY | LEU | LYS |
Entity 2, entity_2 443 residues - 48256.020 Da.
| 1 | MET | ASN | HIS | LYS | VAL | HIS | HIS | HIS | HIS | HIS | ||||
| 2 | HIS | MET | GLN | VAL | SER | VAL | GLU | THR | THR | GLN | ||||
| 3 | GLY | LEU | GLY | ARG | ARG | VAL | THR | ILE | THR | ILE | ||||
| 4 | ALA | ALA | ASP | SER | ILE | GLU | THR | ALA | VAL | LYS | ||||
| 5 | SER | GLU | LEU | VAL | ASN | VAL | ALA | LYS | LYS | VAL | ||||
| 6 | ARG | ILE | ASP | GLY | PHE | ARG | LYS | GLY | LYS | VAL | ||||
| 7 | PRO | MET | ASN | ILE | VAL | ALA | GLN | ARG | TYR | GLY | ||||
| 8 | ALA | SER | VAL | ARG | GLN | ASP | VAL | LEU | GLY | ASP | ||||
| 9 | LEU | MET | SER | ARG | ASN | PHE | ILE | ASP | ALA | ILE | ||||
| 10 | ILE | LYS | GLU | LYS | ILE | ASN | PRO | ALA | GLY | ALA | ||||
| 11 | PRO | THR | TYR | VAL | PRO | GLY | GLU | TYR | LYS | LEU | ||||
| 12 | GLY | GLU | ASP | PHE | THR | TYR | SER | VAL | GLU | PHE | ||||
| 13 | GLU | VAL | TYR | PRO | GLU | VAL | GLU | LEU | GLN | GLY | ||||
| 14 | LEU | GLU | ALA | ILE | GLU | VAL | GLU | LYS | PRO | ILE | ||||
| 15 | VAL | GLU | VAL | THR | ASP | ALA | ASP | VAL | ASP | GLY | ||||
| 16 | MET | LEU | ASP | THR | LEU | ARG | LYS | GLN | GLN | ALA | ||||
| 17 | THR | TRP | LYS | GLU | LYS | ASP | GLY | ALA | VAL | GLU | ||||
| 18 | ALA | GLU | ASP | ARG | VAL | THR | ILE | ASP | PHE | THR | ||||
| 19 | GLY | SER | VAL | ASP | GLY | GLU | GLU | PHE | GLU | GLY | ||||
| 20 | GLY | LYS | ALA | SER | ASP | PHE | VAL | LEU | ALA | MET | ||||
| 21 | GLY | GLN | GLY | ARG | MET | ILE | PRO | GLY | PHE | GLU | ||||
| 22 | ASP | GLY | ILE | LYS | GLY | HIS | LYS | ALA | GLY | GLU | ||||
| 23 | GLU | PHE | THR | ILE | ASP | VAL | THR | PHE | PRO | GLU | ||||
| 24 | GLU | TYR | HIS | ALA | GLU | ASN | LEU | LYS | GLY | LYS | ||||
| 25 | ALA | ALA | LYS | PHE | ALA | ILE | ASN | LEU | LYS | LYS | ||||
| 26 | VAL | GLU | GLU | ARG | GLU | LEU | PRO | GLU | LEU | THR | ||||
| 27 | ALA | GLU | PHE | ILE | LYS | ARG | PHE | GLY | VAL | GLU | ||||
| 28 | ASP | GLY | SER | VAL | GLU | GLY | LEU | ARG | ALA | GLU | ||||
| 29 | VAL | ARG | LYS | ASN | MET | GLU | ARG | GLU | LEU | LYS | ||||
| 30 | SER | ALA | ILE | ARG | ASN | ARG | VAL | LYS | SER | GLN | ||||
| 31 | ALA | ILE | GLU | GLY | LEU | VAL | LYS | ALA | ASN | ASP | ||||
| 32 | ILE | ASP | VAL | PRO | ALA | ALA | LEU | ILE | ASP | SER | ||||
| 33 | GLU | ILE | ASP | VAL | LEU | ARG | ARG | GLN | ALA | ALA | ||||
| 34 | GLN | ARG | PHE | GLY | GLY | ASN | GLU | LYS | GLN | ALA | ||||
| 35 | LEU | GLU | LEU | PRO | ARG | GLU | LEU | PHE | GLU | GLU | ||||
| 36 | GLN | ALA | LYS | ARG | ARG | VAL | VAL | VAL | GLY | LEU | ||||
| 37 | LEU | LEU | GLY | GLU | VAL | ILE | ARG | THR | ASN | GLU | ||||
| 38 | LEU | LYS | ALA | ASP | GLU | GLU | ARG | VAL | LYS | GLY | ||||
| 39 | LEU | ILE | GLU | GLU | MET | ALA | SER | ALA | TYR | GLU | ||||
| 40 | ASP | PRO | LYS | GLU | VAL | ILE | GLU | PHE | TYR | SER | ||||
| 41 | LYS | ASN | LYS | GLU | LEU | MET | ASP | ASN | MET | ARG | ||||
| 42 | ASN | VAL | ALA | LEU | GLU | GLU | GLN | ALA | VAL | GLU | ||||
| 43 | ALA | VAL | LEU | ALA | LYS | ALA | LYS | VAL | THR | GLU | ||||
| 44 | LYS | GLU | THR | THR | PHE | ASN | GLU | LEU | MET | ASN | ||||
| 45 | GLN | GLN | ALA |
Samples:
sample_1: entity_1, [U-100% 13C; U-100% 15N], 0.5 mM; entity_2, [U-100% 13C; U-100% 15N], 0.5 mM; potassium chloride 100 mM; BME 3 mM; potassium phosphate 20 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 273 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 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C HMQC-NOESY_HMQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HMQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY v3.113, Goddard - chemical shift assignment
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
OLIVIA v1.16, Olivia, Yokochi Masashi - chemical shift assignment
CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution
TOPSPIN v3.1, Bruker Biospin - collection
VNMRJ, Varian - collection
X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution
TALOSN, Shen and Bax - geometry optimization
PSVS v1.5, Bhattacharya and Montelione - validation
NMR spectrometers:
- Bruker Avance 700 MHz
- Bruker Avance 600 MHz
- Varian INOVA 600 MHz
- Varian INOVA 800 MHz
Related Database Links:
| PDB | |
| DBJ | BAB33856 BAE76164 BAG75928 BAI23756 BAI29227 BAB33913 BAD98926 BAE76216 BAG75986 BAI23810 |
| EMBL | CAA28257 CAP74918 CAQ30851 CAQ97255 CAR01727 CAP74970 CAQ30908 CAQ97312 CAR01780 CAR06670 |
| GB | AAA24363 AAA24364 AAA24365 AAA24366 AAA24367 AAA62791 AAB40192 AAC73539 AAG54786 AAN42037 |
| REF | NP_308460 NP_414917 NP_706185 WP_000089619 WP_000089625 NP_286178 NP_308517 NP_414970 NP_706330 NP_752485 |
| SP | P00634 A1A8A5 A7ZIJ4 A7ZX94 B1J012 B1LJJ3 |
| BMRB | 19835 19836 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts