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BMRB: 16590

2KQ6

protein x

Authors

Petri, E.T., Celic, A., Kennedy, S.D., Ehrlich, B.E., Boggon, T.J., Hodsdon, M.E.

Assembly

EF-hand domain of polycystin-2

Entity

1. EF-hand domain of polycystin-2 (polymer, Thiol state: not present), 78 monomers, 8996.474 Da Detail

NTVDDISESL RQGGGKLNFD ELRQDLKGKG HTDAEIEAIF TKYDQDGDQE LTEHEHQQMR DDLEKEREDL DLDHSSLP

Formula weight

8996.474 Da

Source organism

Exptl. method

Refine. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 73.2 %, Completeness (bb): 73.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.2 % (649 of 887)	86.5 % (404 of 467)	50.1 % (168 of 335)	90.6 % (77 of 85)
Backbone	73.4 % (342 of 466)	93.8 % (151 of 161)	52.2 % (119 of 228)	93.5 % (72 of 77)
Sidechain	72.8 % (359 of 493)	82.7 % (253 of 306)	56.4 % (101 of 179)	62.5 % (5 of 8)
Aromatic	38.6 % (17 of 44)	50.0 % (11 of 22)	27.3 % (6 of 22)
Methyl	76.6 % (49 of 64)	93.8 % (30 of 32)	59.4 % (19 of 32)

1. EF-hand domain of polycystin-2

NTVDDISESL RQGGGKLNFD ELRQDLKGKG HTDAEIEAIF TKYDQDGDQE LTEHEHQQMR DDLEKEREDL DLDHSSLP

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	EF-hand domain of polycystin-2	[U-13C; U-15N]		1 mM
2	D2O	natural abundance		5 %
3	sodium azide	natural abundance		0.05 %
4	PMSF	natural abundance		10 uM
5	TRIS pH7.4	natural abundance		2 mM
6	sodium chloride	natural abundance		150 mM
7	Ca2+	natural abundance		20 mM
8	D2O	natural abundance		95 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
9	EF-hand domain of polycystin-2	[U-15N]		1 mM
10	TRIS pH7.4	natural abundance		2 mM
11	Ca2+	natural abundance		20 mM
12	sodium chloride	natural abundance		150 mM
13	D2O	natural abundance		5 %
14	PMSF	natural abundance		10 uM
15	H2O	natural abundance		95 %

LACS Plot; CA

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KQ6, Strand ID: A Detail

Release date

2010-05-05

Citation

Structure of the EF-hand domain of polycystin-2 suggests a mechanism for Ca2+-dependent regulation of polycystin-2 channel activity
Petri, E.T., Celic, A., Kennedy, S.D., Ehrlich, B.E., Boggon, T.J., Hodsdon, M.E.
Proc. Natl. Acad. Sci. U. S. A. (2010), 107, 9176-9181, PubMed 20439752 , DOI 10.1073/pnas.0912295107 , Abstract

Related entities 1. EF-hand domain of polycystin-2, : 1 : 5 : 3 : 16 entities Detail

Interaction partners 1. EF-hand domain of polycystin-2, : 21 interactors Detail

More details for 21 interactors identified by 9 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
9	EF-hand domain of polycystin-2	[U-15N]		1 mM
10	TRIS pH7.4	natural abundance		2 mM
11	Ca2+	natural abundance		20 mM
12	sodium chloride	natural abundance		150 mM
13	D2O	natural abundance		5 %
14	PMSF	natural abundance		10 uM
15	H2O	natural abundance		95 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	EF-hand domain of polycystin-2	[U-13C; U-15N]		1 mM
2	D2O	natural abundance		5 %
3	sodium azide	natural abundance		0.05 %
4	PMSF	natural abundance		10 uM
5	TRIS pH7.4	natural abundance		2 mM
6	sodium chloride	natural abundance		150 mM
7	Ca2+	natural abundance		20 mM
8	D2O	natural abundance		95 %

3 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
9	EF-hand domain of polycystin-2	[U-15N]		1 mM
10	TRIS pH7.4	natural abundance		2 mM
11	Ca2+	natural abundance		20 mM
12	sodium chloride	natural abundance		150 mM
13	D2O	natural abundance		5 %
14	PMSF	natural abundance		10 uM
15	H2O	natural abundance		95 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	EF-hand domain of polycystin-2	[U-13C; U-15N]		1 mM
2	D2O	natural abundance		5 %
3	sodium azide	natural abundance		0.05 %
4	PMSF	natural abundance		10 uM
5	TRIS pH7.4	natural abundance		2 mM
6	sodium chloride	natural abundance		150 mM
7	Ca2+	natural abundance		20 mM
8	D2O	natural abundance		95 %

5 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	EF-hand domain of polycystin-2	[U-13C; U-15N]		1 mM
2	D2O	natural abundance		5 %
3	sodium azide	natural abundance		0.05 %
4	PMSF	natural abundance		10 uM
5	TRIS pH7.4	natural abundance		2 mM
6	sodium chloride	natural abundance		150 mM
7	Ca2+	natural abundance		20 mM
8	D2O	natural abundance		95 %

6 3D HNCO

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	EF-hand domain of polycystin-2	[U-13C; U-15N]		1 mM
2	D2O	natural abundance		5 %
3	sodium azide	natural abundance		0.05 %
4	PMSF	natural abundance		10 uM
5	TRIS pH7.4	natural abundance		2 mM
6	sodium chloride	natural abundance		150 mM
7	Ca2+	natural abundance		20 mM
8	D2O	natural abundance		95 %

7 3D HNCA

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	EF-hand domain of polycystin-2	[U-13C; U-15N]		1 mM
2	D2O	natural abundance		5 %
3	sodium azide	natural abundance		0.05 %
4	PMSF	natural abundance		10 uM
5	TRIS pH7.4	natural abundance		2 mM
6	sodium chloride	natural abundance		150 mM
7	Ca2+	natural abundance		20 mM
8	D2O	natural abundance		95 %

8 3D HNCACB

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	EF-hand domain of polycystin-2	[U-13C; U-15N]		1 mM
2	D2O	natural abundance		5 %
3	sodium azide	natural abundance		0.05 %
4	PMSF	natural abundance		10 uM
5	TRIS pH7.4	natural abundance		2 mM
6	sodium chloride	natural abundance		150 mM
7	Ca2+	natural abundance		20 mM
8	D2O	natural abundance		95 %

9 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	EF-hand domain of polycystin-2	[U-13C; U-15N]		1 mM
2	D2O	natural abundance		5 %
3	sodium azide	natural abundance		0.05 %
4	PMSF	natural abundance		10 uM
5	TRIS pH7.4	natural abundance		2 mM
6	sodium chloride	natural abundance		150 mM
7	Ca2+	natural abundance		20 mM
8	D2O	natural abundance		95 %

10 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	EF-hand domain of polycystin-2	[U-13C; U-15N]		1 mM
2	D2O	natural abundance		5 %
3	sodium azide	natural abundance		0.05 %
4	PMSF	natural abundance		10 uM
5	TRIS pH7.4	natural abundance		2 mM
6	sodium chloride	natural abundance		150 mM
7	Ca2+	natural abundance		20 mM
8	D2O	natural abundance		95 %

11 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	EF-hand domain of polycystin-2	[U-13C; U-15N]		1 mM
2	D2O	natural abundance		5 %
3	sodium azide	natural abundance		0.05 %
4	PMSF	natural abundance		10 uM
5	TRIS pH7.4	natural abundance		2 mM
6	sodium chloride	natural abundance		150 mM
7	Ca2+	natural abundance		20 mM
8	D2O	natural abundance		95 %

12 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
9	EF-hand domain of polycystin-2	[U-15N]		1 mM
10	TRIS pH7.4	natural abundance		2 mM
11	Ca2+	natural abundance		20 mM
12	sodium chloride	natural abundance		150 mM
13	D2O	natural abundance		5 %
14	PMSF	natural abundance		10 uM
15	H2O	natural abundance		95 %

13 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
9	EF-hand domain of polycystin-2	[U-15N]		1 mM
10	TRIS pH7.4	natural abundance		2 mM
11	Ca2+	natural abundance		20 mM
12	sodium chloride	natural abundance		150 mM
13	D2O	natural abundance		5 %
14	PMSF	natural abundance		10 uM
15	H2O	natural abundance		95 %

14 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz room temperature, 5 mm, triple resonance (HCN) probe equipped with triple-axis (XYZ) pulsed magnetic field gradients

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	EF-hand domain of polycystin-2	[U-13C; U-15N]		1 mM
2	D2O	natural abundance		5 %
3	sodium azide	natural abundance		0.05 %
4	PMSF	natural abundance		10 uM
5	TRIS pH7.4	natural abundance		2 mM
6	sodium chloride	natural abundance		150 mM
7	Ca2+	natural abundance		20 mM
8	D2O	natural abundance		95 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16590_2kq6.nef
Input source #2: Coordindates	2kq6.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--------
NTVDDISESLRQGGGKLNFDELRQDLKGKGHTDAEIEAIFTKYDQDGDQELTEHEHQQMRDDLEKEREDLDLDHSSLP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NTVDDISESLRQGGGKLNFDELRQDLKGKGHTDAEIEAIFTKYDQDGDQELTEHEHQQMRDDLEKEREDLDLDHSSLP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	78	0	0	100.0

Content subtype: combined_16590_2kq6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	632		97.4 (chain: A, length: 78)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1013 (1)	noe	85.9 (chain: A, length: 78)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	148 (148)	.	100.0 (chain: A, length: 78)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	59 (59)	.	75.6 (chain: A, length: 78)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 399
  - ¹³C chemical shifts: 157
  - ¹⁵N chemical shifts: 76
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 85.9%
- Total number of restraints: 993
- Weight of restraints: 1.0 (993)
- Potential type of restraints: square-well-parabolic (993)
- Range of distance target values: 2.21, 3.9 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 100.0%
- Total number of restraints: 148
- Total number of restraints per polymer type: 148
- Weight of restraints: 1.0 (148)
- Potential type of restraints: square-well-parabolic (148)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 75.6%

--------10--------20--------30--------40--------50--------60--------70--------
NTVDDISESLRQGGGKLNFDELRQDLKGKGHTDAEIEAIFTKYDQDGDQELTEHEHQQMRDDLEKEREDLDLDHSSLP
  |  | |      ||||||||||||||||||||||||||||||||| ||||||| | ||||||||||||||    | 
..V..I.E......GKLNFDELRQDLKGKGHTDAEIEAIFTKYDQDG.QELTEHE.Q.MRDDLEKEREDLDL....L 
--------10--------20--------30--------40--------50--------60--------70-------

Total number of restraints: 59
Potential type of restraints: undefined (59)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords protein x