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Found 1 Document (1.486 seconds)

BMRB: 30492

6E26

NMR solution structure of the CARD9 CARD

Authors

Holliday, M.J., Dueber, E.C., Fairbrother, W.J.

Assembly

Caspase recruitment domain-containing protein 9

Entity

1. Caspase recruitment domain-containing protein 9 (polymer, Thiol state: all free), 97 monomers, 11250.76 Da Detail

MSDYENDDEC WSVLEGFRVT LTSVIDPSRI TPYLRQCKVL NPDDEEQVLS DPNLVIRKRK VGVLLDILQR TGHKGYVAFL ESLELYYPQL YKKVTGK

Formula weight

11250.76 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 96.3 %, Completeness (bb): 96.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (1127 of 1170)	96.1 % (587 of 611)	96.7 % (444 of 459)	96.0 % (96 of 100)
Backbone	96.7 % (553 of 572)	96.4 % (187 of 194)	97.2 % (278 of 286)	95.7 % (88 of 92)
Sidechain	96.2 % (664 of 690)	95.9 % (400 of 417)	96.6 % (256 of 265)	100.0 % (8 of 8)
Aromatic	92.9 % (78 of 84)	92.9 % (39 of 42)	92.7 % (38 of 41)	100.0 % (1 of 1)
Methyl	96.7 % (116 of 120)	96.7 % (58 of 60)	96.7 % (58 of 60)

1. entity 1

MSDYENDDEC WSVLEGFRVT LTSVIDPSRI TPYLRQCKVL NPDDEEQVLS DPNLVIRKRK VGVLLDILQR TGHKGYVAFL ESLELYYPQL YKKVTGK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.4 mM [U-13C; U-15N] CARD9 CARD, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	CARD9 CARD	[U-13C; U-15N]		0.4 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.58 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.58 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.62 ppm, Outliers: 1 Detail

Release date

2018-08-02

Citation

Picomolar zinc binding modulates formation of Bcl10-nucleating assemblies of the caspase recruitment domain (CARD) of CARD9
Holliday, M.J., Ferrao, R., de Leon Boenig, G., Estevez, A., Helgason, E., Rohou, A., Dueber, E.C., Fairbrother, W.J.
J. Biol. Chem. (2018), 293, 16803-16817, PubMed 30206119 , DOI 10.1074/jbc.RA118.004821 , Abstract

Entries sharing articles BMRB: 1, EMDB: 1 entries Detail

  BMRB: 30491 released on 2018-08-02
    Title NMR solution structure of the CARD9 CARD bound to zinc
  EMDB: 8976 released on 2018-08-22
    Title CARD9 CARD helical filament

Related entities 1. Caspase recruitment domain-containing protein 9, : 1 : 3 : 2 : 38 entities Detail

Interaction partners 1. Caspase recruitment domain-containing protein 9, : 75 interactors Detail

More details for 75 interactors identified by 8 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM

2 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM

3 3D HNCACB

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM

4 3D HNCO

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM

5 3D H(CCO)NH

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM

6 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM

7 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM

8 3D HN(CO)CA

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM

9 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM

10 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.4 mM [U-13C; U-15N] CARD9 CARD, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	CARD9 CARD	[U-13C; U-15N]		0.4 mM

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.4 mM [U-13C; U-15N] CARD9 CARD, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	CARD9 CARD	[U-13C; U-15N]		0.4 mM

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30492_6e26.nef
Input source #2: Coordindates	6e26.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-------
MSDYENDDECWSVLEGFRVTLTSVIDPSRITPYLRQCKVLNPDDEEQVLSDPNLVIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSDYENDDECWSVLEGFRVTLTSVIDPSRITPYLRQCKVLNPDDEEQVLSDPNLVIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	97	0	0	100.0

Content subtype: combined_30492_6e26.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1139		99.0 (chain: A, length: 97)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	1931 (1)	noe	96.9 (chain: A, length: 97)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	66 (1)	hbond	53.6 (chain: A, length: 97)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	140 (140)	.	86.6 (chain: A, length: 97)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 97, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 594
  - ¹³C chemical shifts: 449
  - ¹⁵N chemical shifts: 96
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
71	THR	HG1	5.456
82	SER	HG	4.867

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	611	592	96.9
¹³C chemical shifts	459	449	97.8
¹⁵N chemical shifts	106	96	90.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	194	189	97.4
¹³C chemical shifts	194	190	97.9
¹⁵N chemical shifts	92	88	95.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	417	403	96.6
¹³C chemical shifts	265	259	97.7
¹⁵N chemical shifts	14	8	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	60	98.4
¹³C chemical shifts	61	60	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	39	92.9
¹³C chemical shifts	41	38	92.7
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 97, Sequence coverage: 96.9%
- Total number of restraints: 1930
- Weight of restraints: 1.0 (1930)
- Potential type of restraints: square-well-parabolic (1930)
- Range of distance target values: 1.64, 3.3 (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: 97, Sequence coverage: 53.6%
  - Total number of restraints: 66
  - Weight of restraints: 1.0 (66)
  - Potential type of restraints: square-well-parabolic (66)
  - Range of distance target values: 1.0, 1.5 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 97, Sequence coverage: 86.6%
- Total number of restraints: 140
- Total number of restraints per polymer type: 140
- Weight of restraints: 1.0 (140)
- Potential type of restraints: square-well-parabolic (140)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CARD, SIGNALING PROTEIN, innate immunity

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Found 1 Document (1.486 seconds)

BMRB: 30492

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1, EMDB: 1 entries Detail

Related entities 1. Caspase recruitment domain-containing protein 9, : 1 : 3 : 2 : 38 entities Detail

Interaction partners 1. Caspase recruitment domain-containing protein 9, : 75 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 5 contents Detail