BMRBj - BMREntryMaster

Found 1 Document (0.883 seconds)

BMRB: 25943

2NAQ

3D NMR solution structure of NLRP3 PYD

Authors

de Alba, E., Oroz, J.

Assembly

NLRP3 PYD

Entity

1. NLRP3 PYD (polymer), 91 monomers, 10625.15 Da Detail

MASTRCKLAR YLEDLEDVDL KKFKMHLEDY PPQKGCIPLP RGQTEKADHV DLATLMIDFN GEEKAWAMAV WIFAAINRRD LYEKAKRDEP K

Formula weight

10625.15 Da

Source organism

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.8 %, Completeness: 81.8 %, Completeness (bb): 82.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.8 % (901 of 1102)	88.6 % (515 of 581)	70.2 % (301 of 429)	92.4 % (85 of 92)
Backbone	82.1 % (440 of 536)	96.7 % (174 of 180)	67.4 % (182 of 270)	97.7 % (84 of 86)
Sidechain	82.0 % (536 of 654)	83.5 % (335 of 401)	81.0 % (200 of 247)	16.7 % (1 of 6)
Aromatic	70.9 % (61 of 86)	69.8 % (30 of 43)	75.6 % (31 of 41)	0.0 % (0 of 2)
Methyl	100.0 % (90 of 90)	100.0 % (45 of 45)	100.0 % (45 of 45)

1. entity

MASTRCKLAR YLEDLEDVDL KKFKMHLEDY PPQKGCIPLP RGQTEKADHV DLATLMIDFN GEEKAWAMAV WIFAAINRRD LYEKAKRDEP K

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		100.0 ~ 200.0 uM
2	TCEP	[U-2H]		5 mM
3	sodium azide	natural abundance		100 uM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 0.25 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.25 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.0 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2NAQ, Strand ID: A Detail

Release date

2016-07-24

Citation

Asc Pyrin Domain Self-Associates and Binds Nlrp3 Using Equivalent Binding Interfaces
Oroz, J., Barrera-Vilarmau, S., Alfonso, C., Rivas, G., de Alba, E.
J. Biol. Chem. (2016), 291, 19487-19501, PubMed 27432880 , DOI 10.1074/jbc.M116.741082 , Abstract

Related entities 1. NLRP3 PYD, : 1 : 7 : 1 : 100 entities Detail

Interaction partners 1. NLRP3 PYD, : 10 interactors Detail

More details for 10 interactors identified by 8 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		100.0 ~ 200.0 uM
2	TCEP	[U-2H]		5 mM
3	sodium azide	natural abundance		100 uM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

2 3D HNCACB

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		100.0 ~ 200.0 uM
2	TCEP	[U-2H]		5 mM
3	sodium azide	natural abundance		100 uM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		100.0 ~ 200.0 uM
2	TCEP	[U-2H]		5 mM
3	sodium azide	natural abundance		100 uM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		100.0 ~ 200.0 uM
2	TCEP	[U-2H]		5 mM
3	sodium azide	natural abundance		100 uM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

5 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		100.0 ~ 200.0 uM
2	TCEP	[U-2H]		5 mM
3	sodium azide	natural abundance		100 uM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		100.0 ~ 200.0 uM
2	TCEP	[U-2H]		5 mM
3	sodium azide	natural abundance		100 uM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		100.0 ~ 200.0 uM
2	TCEP	[U-2H]		5 mM
3	sodium azide	natural abundance		100 uM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		100.0 ~ 200.0 uM
2	TCEP	[U-2H]		5 mM
3	sodium azide	natural abundance		100 uM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

9 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Avance III

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		100.0 ~ 200.0 uM
2	TCEP	[U-2H]		5 mM
3	sodium azide	natural abundance		100 uM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25943_2naq.nef
Input source #2: Coordindates	2naq.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--------80--------90-
MASTRCKLARYLEDLEDVDLKKFKMHLEDYPPQKGCIPLPRGQTEKADHVDLATLMIDFNGEEKAWAMAVWIFAAINRRDLYEKAKRDEPK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MASTRCKLARYLEDLEDVDLKKFKMHLEDYPPQKGCIPLPRGQTEKADHVDLATLMIDFNGEEKAWAMAVWIFAAINRRDLYEKAKRDEPK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	91	0	0	100.0

Content subtype: combined_25943_2naq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	891		97.8 (chain: A, length: 91)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1553 (1)	noe	98.9 (chain: A, length: 91)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	66 (1)	hbond	59.3 (chain: A, length: 91)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	162 (162)	.	100.0 (chain: A, length: 91)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 97.8%
- Total number of assignments
  - ¹H chemical shifts: 518
  - ¹³C chemical shifts: 289
  - ¹⁵N chemical shifts: 84
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 98.9%
- Total number of restraints: 1497
- Weight of restraints: 1.0 (1497)
- Potential type of restraints: square-well-parabolic (1497)
- Range of distance target values: 1.95, 5.85 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 59.3%
  - Total number of restraints: 66
  - Weight of restraints: 1.0 (66)
  - Potential type of restraints: square-well-parabolic (66)
  - Range of distance target values: 2.2, 3.1 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 100.0%
- Total number of restraints: 162
- Total number of restraints per polymer type: 162
- Weight of restraints: 1.0 (162)
- Potential type of restraints: square-well-parabolic (162)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Death Domain Superfamily, PYD