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BMRB: 19732

2MJM

The solution NMR structure of the NLRC5 caspase recruitment domain (CARD)

Authors

Gutte, P.G.M., Zerbe, O.

Assembly

NLRC5 caspase recruitment domain (CARD)

Entity

1. NLRC5 caspase recruitment domain (CARD) (polymer, Thiol state: all free), 101 monomers, 11659.32 Da Detail

GPLGSMDAES IRLNNENLWA WLVRLLSKNP EWLSAKLRSF LPTMDLDCSY EPSNPEVIHR QLNRLFAQGM ATWKSFINDL CFELDVPLDM EIPLVSIWGP R

Formula weight

11659.32 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.0 %, Completeness: 84.0 %, Completeness (bb): 86.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.0 % (1027 of 1222)	80.7 % (515 of 638)	86.6 % (413 of 477)	92.5 % (99 of 107)
Backbone	86.8 % (512 of 590)	79.8 % (158 of 198)	89.3 % (267 of 299)	93.5 % (87 of 93)
Sidechain	82.7 % (603 of 729)	81.1 % (357 of 440)	85.1 % (234 of 275)	85.7 % (12 of 14)
Aromatic	70.5 % (79 of 112)	71.4 % (40 of 56)	66.7 % (34 of 51)	100.0 % (5 of 5)
Methyl	82.5 % (94 of 114)	78.9 % (45 of 57)	86.0 % (49 of 57)

1. entity

GPLGSMDAES IRLNNENLWA WLVRLLSKNP EWLSAKLRSF LPTMDLDCSY EPSNPEVIHR QLNRLFAQGM ATWKSFINDL CFELDVPLDM EIPLVSIWGP R

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	NLRC5_CARD	[U-100% 13C; U-100% 15N]		600 uM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	potassium chloride	natural abundance		50 mM
5	TCEP	natural abundance		2 mM
6	H2O	natural abundance		95 %
7	D2O	[U-100% 2H]		5 %

LACS Plot; CA

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.08 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.22 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2014-05-12

Citation

The solution NMR structure of the NLRC5 caspase recruitment domain (CARD) reveals unusual structural features
Gutte, P.G.M., Jurt, S., Gruetter, M.G., Zerbe, O.
Biochemistry, 53, 3106-3117, DOI 10.1021/bi500177x

Related entities 1. NLRC5 caspase recruitment domain (CARD), : 1 : 2 : 9 entities Detail

Interaction partners 1. NLRC5 caspase recruitment domain (CARD), : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	NLRC5_CARD	[U-100% 13C; U-100% 15N]		600 uM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	potassium chloride	natural abundance		50 mM
5	TCEP	natural abundance		2 mM
6	H2O	natural abundance		95 %
7	D2O	[U-100% 2H]		5 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	NLRC5_CARD	[U-100% 13C; U-100% 15N]		600 uM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	potassium chloride	natural abundance		50 mM
5	TCEP	natural abundance		2 mM
6	H2O	natural abundance		95 %
7	D2O	[U-100% 2H]		5 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	NLRC5_CARD	[U-100% 13C; U-100% 15N]		600 uM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	potassium chloride	natural abundance		50 mM
5	TCEP	natural abundance		2 mM
6	H2O	natural abundance		95 %
7	D2O	[U-100% 2H]		5 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	NLRC5_CARD	[U-100% 13C; U-100% 15N]		600 uM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	potassium chloride	natural abundance		50 mM
5	TCEP	natural abundance		2 mM
6	H2O	natural abundance		95 %
7	D2O	[U-100% 2H]		5 %

5 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	NLRC5_CARD	[U-100% 13C; U-100% 15N]		600 uM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	potassium chloride	natural abundance		50 mM
5	TCEP	natural abundance		2 mM
6	H2O	natural abundance		95 %
7	D2O	[U-100% 2H]		5 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	NLRC5_CARD	[U-100% 13C; U-100% 15N]		600 uM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	potassium chloride	natural abundance		50 mM
5	TCEP	natural abundance		2 mM
6	H2O	natural abundance		95 %
7	D2O	[U-100% 2H]		5 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	NLRC5_CARD	[U-100% 13C; U-100% 15N]		600 uM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	potassium chloride	natural abundance		50 mM
5	TCEP	natural abundance		2 mM
6	H2O	natural abundance		95 %
7	D2O	[U-100% 2H]		5 %

8 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	NLRC5_CARD	[U-100% 13C; U-100% 15N]		600 uM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	potassium chloride	natural abundance		50 mM
5	TCEP	natural abundance		2 mM
6	H2O	natural abundance		95 %
7	D2O	[U-100% 2H]		5 %

9 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	NLRC5_CARD	[U-100% 13C; U-100% 15N]		600 uM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	potassium chloride	natural abundance		50 mM
5	TCEP	natural abundance		2 mM
6	H2O	natural abundance		95 %
7	D2O	[U-100% 2H]		5 %

10 HB(CBCGCD)HD

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	NLRC5_CARD	[U-100% 13C; U-100% 15N]		600 uM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	potassium chloride	natural abundance		50 mM
5	TCEP	natural abundance		2 mM
6	H2O	natural abundance		95 %
7	D2O	[U-100% 2H]		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19732_2mjm.nef
Input source #2: Coordindates	2mjm.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-------100
GPLGSMDAESIRLNNENLWAWLVRLLSKNPEWLSAKLRSFLPTMDLDCSYEPSNPEVIHRQLNRLFAQGMATWKSFINDLCFELDVPLDMEIPLVSIWGP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSMDAESIRLNNENLWAWLVRLLSKNPEWLSAKLRSFLPTMDLDCSYEPSNPEVIHRQLNRLFAQGMATWKSFINDLCFELDVPLDMEIPLVSIWGP

-
R
|
R

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	101	0	0	100.0

Content subtype: combined_19732_2mjm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1104		95.0 (chain: A, length: 101)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1599 (1)	noe	94.1 (chain: A, length: 101)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	391 (389)	.	100.0 (chain: A, length: 101)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 95.0%
- Total number of assignments
  - ¹H chemical shifts: 576
  - ¹³C chemical shifts: 429
  - ¹⁵N chemical shifts: 99
- 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: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 94.1%
- Total number of restraints: 1599
- Weight of restraints: 1.0 (1599)
- Potential type of restraints: upper-bound-parabolic (1599)
- Range of distance target values: 2.4, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 100.0%
- Total number of restraints: 389
- Total number of restraints per polymer type: 389
- Weight of restraints: 1.0 (389)
- Potential type of restraints: square-well-parabolic (389)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CARD, NLRC5, RIG-I, Solution NMR