BMRBj - BMREntryMaster

Found 1 Document (0.725 seconds)

BMRB: 15268

2JQ3

Structure and Dynamics of Human Apolipoprotein C-III

Authors

Gangabadage, C.S., Zdunek, J., Tessari, M., Nilsson, S., Olivecrona, G., Wijmenga, S.S.

Assembly

ApoCIII

Entity

1. ApoCIII (polymer, Thiol state: not present), 79 monomers, 8764.554 Da Detail

SEAEDASLLS FMQGYMKHAT KTAKDALSSV QESQVAQQAR GWVTDGFSSL KDYWSTVKDK FSEFWDLDPE VRPTSAVAA

Formula weight

8764.554 Da

Source organism

Exptl. method

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 53.2 %, Completeness (bb): 98.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	53.2 % (477 of 896)	35.7 % (164 of 460)	67.2 % (236 of 351)	90.6 % (77 of 85)
Backbone	98.7 % (464 of 470)	96.9 % (154 of 159)	99.6 % (233 of 234)	100.0 % (77 of 77)
Sidechain	17.7 % (89 of 502)	3.3 % (10 of 301)	40.9 % (79 of 193)	0.0 % (0 of 8)
Aromatic	0.0 % (0 of 96)	0.0 % (0 of 48)	0.0 % (0 of 45)	0.0 % (0 of 3)
Methyl	13.5 % (10 of 74)	0.0 % (0 of 37)	27.0 % (10 of 37)

1. Apolipoprotein CIII

SEAEDASLLS FMQGYMKHAT KTAKDALSSV QESQVAQQAR GWVTDGFSSL KDYWSTVKDK FSEFWDLDPE VRPTSAVAA

Show sample condition

Sample #1

Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

Sample #2

Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle "in 4 % stretched polyacrylamide gel 37.5:1 w/w acrlamide:bisacrylamide"

#	Name	Isotope labeling	Type	Concentration
4	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
5	SDS_d25	[U-2H]		180 mM
6	Sodium acetate buffer			50 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2JQ3, Strand ID: A Detail

Release date

2008-06-11

Citation

Structure and dynamics of human apolipoprotein CIII
Gangabadage, C.S., Zdunek, J., Tessari, M., Nilsson, S., Olivecrona, G., Wijmenga, S.S.
J. Biol. Chem. (2008), 283, 17416-17427, PubMed 18408013 , DOI 10.1074/jbc.M800756200 , Abstract

Related entities 1. ApoCIII, : 1 : 2 : 17 entities Detail

Interaction partners 1. ApoCIII, : 6 interactors Detail

More details for 6 interactors identified by 2 citations

Experiments performed 15 experiments Detail

1 CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

2 HNCACB

Instrument

Varian INOVA - 600 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

3 HNCO

Instrument

Varian INOVA - 600 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

4 HNHA

Instrument

Varian INOVA - 600 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

5 15N NOESY HSQC

Instrument

Varian INOVA - 800 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

6 15N HSQC NOESY HSQC

Instrument

Varian INOVA - 800 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

7 [15N,1H] HSQC

Instrument

Varian INOVA - 600 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

8 IPAP [15N,1H] HSQC

Instrument

Varian INOVA - 800 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

9 IPAP [15N,1H] HSQC

Instrument

Varian INOVA - 800 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

10 15N NOE

Instrument

Varian INOVA - 600 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

11 15N NOE

Instrument

Varian INOVA - 800 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

12 15N T1

Instrument

Varian INOVA - 600 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

13 15N T1

Instrument

Varian INOVA - 800 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

14 15N T1rho

Instrument

Varian INOVA - 600 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

15 15N T1rho

Instrument

Varian INOVA - 800 MHz Equipped with triple resonance (1H/13C/15N) with XYZ gradient capabilities

Sample

State isotropic, Pressure 1 atm, Temperature 315.7 K, pH 5.0, Details SDS-micelle

#	Name	Isotope labeling	Type	Concentration
1	Apolipoprotein CIII	[U-13C; U-15N]		0.5 mM
2	SDS_d25	[U-2H]		180 mM
3	Sodium acetate buffer			10 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_15268_2jq3.nef
Input source #2: Coordindates	2jq3.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70---------
SEAEDASLLSFMQGYMKHATKTAKDALSSVQESQVAQQARGWVTDGFSSLKDYWSTVKDKFSEFWDLDPEVRPTSAVAA
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SEAEDASLLSFMQGYMKHATKTAKDALSSVQESQVAQQARGWVTDGFSSLKDYWSTVKDKFSEFWDLDPEVRPTSAVAA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	79	0	0	100.0

Content subtype: combined_15268_2jq3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	459		100.0 (chain: A, length: 79)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	188 (1)	noe	96.2 (chain: A, length: 79)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	154 (154)	.	100.0 (chain: A, length: 79)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	OK	70 (70)	.	88.6 (chain: A, length: 79)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 231
  - ¹H chemical shifts: 152
  - ¹⁵N chemical shifts: 76
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 96.2%
- Total number of restraints: 188
- Weight of restraints: 1.0 (188)
- Potential type of restraints: square-well-parabolic (188)
- Range of distance target values: 1.99, 5.36 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 100.0%
- Total number of restraints: 154
- Total number of restraints per polymer type: 154
- Weight of restraints: 1.0 (154)
- Potential type of restraints: square-well-parabolic (154)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 88.6%
- Total number of restraints: 70
- Potential type of restraints: undefined (70)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords ApoCIII, apolipoprotein, dynamics, NMR, receptor, structure