BMRB Entry 19513
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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/BMR19513
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Title: HIV-1 gp41 clade C Membrane Proximal External Region peptide in DPC micelle PubMed: 24075869
Deposition date: 2013-09-20 Original release date: 2013-10-08
Authors: Sun, Zhenyu; Wagner, Gerhard; Reinherz, Ellis; Kim, Mikyung; Song, Likai; Choi, Jaewon; Cheng, Yuxing; Chowdhury, Barnali; Bellot, Gaetan; Shih, William
Citation: Sun, Zhen-Yu; Cheng, Yuxing; Kim, Mikyung; Song, Likai; Choi, Jaewon; Kudahl, Ulrich; Brusic, Vladimir; Chowdhury, Barnali; Yu, Lu; Seaman, Michael; Bellot, Gaetan; Shih, William; Wagner, Gerhard; Reinherz, Ellis. "Disruption of helix-capping residues 671 and 674 reveals a role in HIV-1 entry for a specialized hinge segment of the membrane proximal external region of gp41." J. Mol. Biol. 426, 1095-1108 (2014).
Assembly members:
MPER-Con089, polymer, 27 residues, 3460.006 Da.
Natural source: Common Name: Human immunodeficiency virus 1 Taxonomy ID: 388796 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus Human immunodeficiency virus 1
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
MPER-Con089: EKDLLALDSWKNLWSWFSIT
NWLWYIK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 112 |
| 15N chemical shifts | 32 |
| 1H chemical shifts | 221 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | MPER-Con089 | 1 |
Entities:
Entity 1, MPER-Con089 27 residues - 3460.006 Da.
Consensus sequence peptide from hiv-1 clade C MPER sequences. Residues 657-661 are from gp41 CHR.
| 1 | GLU | LYS | ASP | LEU | LEU | ALA | LEU | ASP | SER | TRP | ||||
| 2 | LYS | ASN | LEU | TRP | SER | TRP | PHE | SER | ILE | THR | ||||
| 3 | ASN | TRP | LEU | TRP | TYR | ILE | LYS |
Samples:
sample_1: MPER-Con089, [U-100% 13C; U-100% 15N], 1 mM; DPC, [U-100% 2H], 100 mM; H2O 90%; D2O 10%
sample_2: MPER-Con089, [U-100% 15N], 1 mM; DPC, [U-100% 2H], 100 mM; H2O 90%; D2O 10%
sample_3: MPER-Con089 1 mM; DPC, [U-100% 2H], 100 mM; D2O 100%
sample_4: MPER-Con089, [U-100% 13C; U-100% 15N], 1 mM; DPC, [U-100% 2H], 100 mM; DNA nanotube 20 mg/mL; H2O 90%; D2O 10%
sample_conditions_1: pH: 6.6; pressure: 1 atm; temperature: 273 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D backbone | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH,H(CCO)NH,HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY,TOCSY | sample_3 | isotropic | sample_conditions_1 |
| Q-J RDC | sample_4 | anisotropic | sample_conditions_1 |
Software:
NMRPipe v9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
CARA v1.8.4, Rochus Keller - chemical shift assignment, data analysis, peak picking
TALOS v+, (TALOS+) Shen, Cornilescu, Delaglio and Bax - data analysis
CYANA v3.0c, Guntert, Mumenthaler and Wuthrich - structure solution
X-PLOR NIH v2.28, Schwieters, Kuszewski, Tjandra and Clore - refinement
NMR spectrometers:
- Bruker Avance 900 MHz
- Bruker Avance 750 MHz
- Bruker Avance 600 MHz
- Varian INOVA 500 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts