BMRB Entry 15268

Name: Structure and Dynamics of Human Apolipoprotein C-III
Published: 2008-06-12

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PDB ID: 2jq3
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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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure and Dynamics of Human Apolipoprotein C-III

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:

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).
PubMed: 18408013

Assembly members:

Assembly members:
Apolipoprotein_CIII, polymer, 79 residues, 8775.728 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET23b

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	231
15N chemical shifts	76
1H chemical shifts	152

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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

SER

2

PHE

MET

GLN

GLY

TYR

MET

LYS

HIS

ALA

THR

3

LYS

THR

ALA

LYS

ASP

ALA

LEU

SER

VAL

4

GLN

GLU

SER

GLN

VAL

ALA

GLN

ALA

ARG

5

GLY

TRP

VAL

THR

ASP

GLY

PHE

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

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

PDB	2JQ3
EMBL	CAA25233 CAA25644 CAA25648 CAA26895
GB	AAA51760 AAA51761 AAB59372 AAB59515 AAH27977
PRF	1204193A
REF	NP_000031 XP_004052228 XP_004052229
SP	P02656
AlphaFold	P02656