BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 15268

Title: Structure and Dynamics of Human Apolipoprotein C-III   PubMed: 18408013

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

Entity Sequences (FASTA):
Apolipoprotein_CIII: SEAEDASLLSFMQGYMKHAT KTAKDALSSVQESQVAQQAR GWVTDGFSSLKDYWSTVKDK FSEFWDLDPEVRPTSAVAA

Data sets:
Data typeCount
13C chemical shifts231
15N chemical shifts76
1H chemical shifts152

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1ApoCIII1

Entities:

Entity 1, ApoCIII 79 residues - 8775.728 Da.

1   SERGLUALAGLUASPALASERLEULEUSER
2   PHEMETGLNGLYTYRMETLYSHISALATHR
3   LYSTHRALALYSASPALALEUSERSERVAL
4   GLNGLUSERGLNVALALAGLNGLNALAARG
5   GLYTRPVALTHRASPGLYPHESERSERLEU
6   LYSASPTYRTRPSERTHRVALLYSASPLYS
7   PHESERGLUPHETRPASPLEUASPPROGLU
8   VALARGPROTHRSERALAVALALAALA

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:

NameSampleSample stateSample conditions
CBCA(CO)NHsample_1isotropicsample_conditions_1
HNCACBsample_1isotropicsample_conditions_1
HNCOsample_1isotropicsample_conditions_1
HNHAsample_1isotropicsample_conditions_1
15N NOESY HSQCsample_1isotropicsample_conditions_1
15N HSQC NOESY HSQCsample_1isotropicsample_conditions_1
[15N,1H] HSQCsample_1isotropicsample_conditions_1
IPAP [15N,1H] HSQCsample_1isotropicsample_conditions_1
IPAP [15N,1H] HSQCsample_1isotropicsample_conditions_2
15N NOEsample_1isotropicsample_conditions_1
15N NOEsample_1isotropicsample_conditions_1
15N T1sample_1isotropicsample_conditions_1
15N T1sample_1isotropicsample_conditions_1
15N T1rhosample_1isotropicsample_conditions_1
15N T1rhosample_1isotropicsample_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