BMRB Entry 15268
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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/BMR15268
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Title: Structure and Dynamics of Human Apolipoprotein C-III PubMed: 18408013
Deposition date: 2007-05-28 Original release date: 2008-06-12
Authors: Gangabadage, Chinthaka; Zdunek, Janusz; Tessari, Marco; Nilsson, Solveig; Olivecrona, Gunilla; Wijmenga, Sybren
Citation: Gangabadage, Chinthaka; Zdunek, Janusz; Tessari, Marco; Nilsson, Solveig; Olivecrona, Gunilla; Wijmenga, Sybren. "Structure and Dynamics of Human Apolipoprotein CIII" J. Biol. Chem. 283, 17416-17427 (2008).
Assembly members:
Apolipoprotein_CIII, polymer, 79 residues, 8775.728 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 Vector: pET23b
Entity Sequences (FASTA):
Apolipoprotein_CIII: SEAEDASLLSFMQGYMKHAT
KTAKDALSSVQESQVAQQAR
GWVTDGFSSLKDYWSTVKDK
FSEFWDLDPEVRPTSAVAA
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 231 |
| 15N chemical shifts | 76 |
| 1H chemical shifts | 152 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | ApoCIII | 1 |
Entities:
Entity 1, ApoCIII 79 residues - 8775.728 Da.
| 1 | SER | GLU | ALA | GLU | ASP | ALA | SER | LEU | LEU | SER | ||||
| 2 | PHE | MET | GLN | GLY | TYR | MET | LYS | HIS | ALA | THR | ||||
| 3 | LYS | THR | ALA | LYS | ASP | ALA | LEU | SER | SER | VAL | ||||
| 4 | GLN | GLU | SER | GLN | VAL | ALA | GLN | GLN | ALA | ARG | ||||
| 5 | GLY | TRP | VAL | THR | ASP | GLY | PHE | SER | SER | LEU | ||||
| 6 | LYS | ASP | TYR | TRP | SER | THR | VAL | LYS | ASP | LYS | ||||
| 7 | PHE | SER | GLU | PHE | TRP | ASP | LEU | ASP | PRO | GLU | ||||
| 8 | VAL | ARG | PRO | THR | SER | ALA | VAL | ALA | ALA |
Samples:
sample_1: Apolipoprotein CIII, [U-13C; U-15N], 0.5 mM; SDS_d25, [U-2H], 180 mM; Sodium acetate buffer 10 mM
sample_2: Apolipoprotein CIII, [U-13C; U-15N], 0.5 mM; SDS_d25, [U-2H], 180 mM; Sodium acetate buffer 50 mM
sample_conditions_1: ionic strength: 0.3 M; pH: 5.0; pressure: 1 atm; temperature: 315.7 K
sample_conditions_2: ionic strength: 0.3 M; pH: 5.0; pressure: 1 atm; temperature: 315.7 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| HNCACB | sample_1 | isotropic | sample_conditions_1 |
| HNCO | sample_1 | isotropic | sample_conditions_1 |
| HNHA | sample_1 | isotropic | sample_conditions_1 |
| 15N NOESY HSQC | sample_1 | isotropic | sample_conditions_1 |
| 15N HSQC NOESY HSQC | sample_1 | isotropic | sample_conditions_1 |
| [15N,1H] HSQC | sample_1 | isotropic | sample_conditions_1 |
| IPAP [15N,1H] HSQC | sample_1 | isotropic | sample_conditions_1 |
| IPAP [15N,1H] HSQC | sample_1 | isotropic | sample_conditions_2 |
| 15N NOE | sample_1 | isotropic | sample_conditions_1 |
| 15N NOE | sample_1 | isotropic | sample_conditions_1 |
| 15N T1 | sample_1 | isotropic | sample_conditions_1 |
| 15N T1 | sample_1 | isotropic | sample_conditions_1 |
| 15N T1rho | sample_1 | isotropic | sample_conditions_1 |
| 15N T1rho | sample_1 | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
XEASY, Bartels et al. - peak picking
TALOS, Cornilescu, Delaglio and Bax - backbone torsion angles from chemical shifts
X-PLOR NIH v2.10, Schwieters, Kuszewski, Tjandra and Clore - Restr. MD caclulations
Monte_Carlo_script, S.Wijmenga (unpublished) - Monte Carlo simulation to fit helical structures to experimental RDCs using dipolar waves formulation of RDCs
Protein Constructor, under development) - Caclulations of hydropobic moment directions, Inverse kinematic for junction of helices, RDC simulation, Program for positioning helices on the micelle
NMR spectrometers:
- Varian INOVA 600 MHz
- Varian INOVA 800 MHz
Related Database Links:
| PDB | |
| EMBL | CAA25233 CAA25644 CAA25648 CAA26895 |
| GB | AAA51760 AAA51761 AAB59372 AAB59515 AAH27977 |
| PRF | 1204193A |
| REF | NP_000031 XP_004052228 XP_004052229 |
| SP | P02656 |
| AlphaFold | P02656 |
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts