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Found 1 Document (1.33 seconds)

BMRB: 30491

6E25

NMR solution structure of the CARD9 CARD bound to zinc

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, entity 1 (polymer, Thiol state: free and other bound), 97 monomers, 11250.76 Da Detail

MSDYENDDEC WSVLEGFRVT LTSVIDPSRI TPYLRQCKVL NPDDEEQVLS DPNLVIRKRK VGVLLDILQR TGHKGYVAFL ESLELYYPQL YKKVTGK

2. Caspase recruitment domain-containing protein 9, entity ZN (non-polymer), 65.409 Da

Total weight

11316.169 Da

Max. entity weight

11250.76 Da

Entity Connection

metal coordination 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:ASP7:OD2	2:ZN1:ZN
2	metal coordination	sing	1:CYS10:SG	2:ZN1:ZN
3	metal coordination	sing	1:HIS73:ND1	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 90.2 %, Completeness (bb): 84.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.2 % (1055 of 1170)	95.6 % (584 of 611)	81.7 % (375 of 459)	96.0 % (96 of 100)
Backbone	84.1 % (481 of 572)	95.9 % (186 of 194)	72.4 % (207 of 286)	95.7 % (88 of 92)
Sidechain	96.4 % (665 of 690)	95.4 % (398 of 417)	97.7 % (259 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	99.2 % (119 of 120)	98.3 % (59 of 60)	100.0 % (60 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, 0.46 mM zinc, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM
2	zinc	none		0.46 mM

Sample #2

Solvent system 50% H2O/50% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-10% 13C; U-100% 15N] CARD9 CARD, 0.46 mM zinc, 50% H2O/50% D2O

#	Name	Isotope labeling	Type	Concentration
3	CARD9 CARD	[U-10% 13C; U-100% 15N]		0.40 mM
4	zinc	none		0.46 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-13C; U-15N] CARD9 CARD, 0.46 mM zinc, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	CARD9 CARD	[U-13C; U-15N]		0.40 mM
6	zinc	none		0.46 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: -0.56 ppm, Outliers: 2 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: -0.56 ppm, Outliers: 2 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: 2 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

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

Interaction partners 1. Caspase recruitment domain-containing protein 9, entity 1, : 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, 0.46 mM zinc, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM
2	zinc	none		0.46 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, 0.46 mM zinc, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM
2	zinc	none		0.46 mM

3 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, 0.46 mM zinc, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM
2	zinc	none		0.46 mM

4 3D HNCA

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, 0.46 mM zinc, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM
2	zinc	none		0.46 mM

5 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 50% H2O/50% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 0.40 mM [U-10% 13C; U-100% 15N] CARD9 CARD, 0.46 mM zinc, 50% H2O/50% D2O

#	Name	Isotope labeling	Type	Concentration
3	CARD9 CARD	[U-10% 13C; U-100% 15N]		0.40 mM
4	zinc	none		0.46 mM

6 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, 0.46 mM zinc, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM
2	zinc	none		0.46 mM

7 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 0.40 mM [U-13C; U-15N] CARD9 CARD, 0.46 mM zinc, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	CARD9 CARD	[U-13C; U-15N]		0.40 mM
6	zinc	none		0.46 mM

8 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 0.40 mM [U-13C; U-15N] CARD9 CARD, 0.46 mM zinc, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	CARD9 CARD	[U-13C; U-15N]		0.40 mM
6	zinc	none		0.46 mM

9 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, 0.46 mM zinc, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM
2	zinc	none		0.46 mM

10 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, 0.46 mM zinc, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM
2	zinc	none		0.46 mM

11 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, 0.46 mM zinc, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM
2	zinc	none		0.46 mM

12 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, 0.46 mM zinc, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CARD9 CARD	[U-13C; U-15N]		0.40 mM
2	zinc	none		0.46 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30491_6e25.nef
Input source #2: Coordindates	6e25.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:7:ASP:OD2	2:1:ZN:ZN	unknown	unknown	n/a
1:10:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:73:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	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_30491_6e25.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1041		99.0 (chain: A, length: 97)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	2005 (1)	noe	97.9 (chain: A, length: 97)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	1 (1)	undefined	No information
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	60 (1)	hbond	48.5 (chain: A, length: 97)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	140 (140)	.	90.7 (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: 591
  - ¹³C chemical shifts: 355
  - ¹⁵N chemical shifts: 95
- 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	5.172
82	SER	HG	4.835

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	611	589	96.4
¹³C chemical shifts	459	355	77.3
¹⁵N chemical shifts	106	95	89.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	194	188	96.9
¹³C chemical shifts	194	96	49.5
¹⁵N chemical shifts	92	87	94.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	417	401	96.2
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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 97, Sequence coverage: 97.9%
- Total number of restraints: 2000
- Weight of restraints: 1.0 (2000)
- Potential type of restraints: square-well-parabolic (2000)
- Range of distance target values: 1.6, 3.3 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: OK
  - Experiment type: undefined
  - Total number of restraints: 1
  - Weight of restraints: 1.0 (1)
  - Potential type of restraints: square-well-parabolic (1)
  - Range of distance target values: 3.4, 3.4 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - 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: 48.5%
    - Total number of restraints: 60
    - Weight of restraints: 1.0 (60)
    - Potential type of restraints: square-well-parabolic (60)
    - Range of distance target values: 1.0, 1.5 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - 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: 90.7%
- 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 (1.33 seconds)

BMRB: 30491

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

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

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

Experiments performed 12 experiments Detail

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NMR combined restraints 6 contents Detail