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BMRB: 18826

2M0V

Complex structure of C-terminal CFTR peptide and extended PDZ2 domain from NHERF1.

Authors

Bhattacharya, S., Ju, J.H., Cowburn, D., Bu, Z.

Assembly

C-terminal CFTR peptide and extended PDZ2 domain from NHERF1

Entity

1. PDZ2 (polymer, Thiol state: all free), 128 monomers, 14079.79 Da Detail

GIDPFTMLRP RLCTMKKGPS GYGFNLHSDK SKPGQFIRSV DPDSPAEASG LRAQDRIVEV NGVCMEGKQH GDVVSAIRAG GDETKLLVVD RETDEFFKKC RVIPSQEHLN GPLPVPFTNG EIQKENSR

2. CFTR (polymer, Thiol state: not present), 5 monomers, 631.6789 Da Detail

QDTRL

Total weight

14711.469 Da

Max. entity weight

14079.79 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.3 %, Completeness (bb): 94.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.3 % (1390 of 1523)	94.5 % (760 of 804)	86.2 % (504 of 585)	94.0 % (126 of 134)
Backbone	94.0 % (731 of 778)	97.4 % (262 of 269)	91.5 % (353 of 386)	94.3 % (116 of 123)
Sidechain	88.1 % (762 of 865)	91.2 % (488 of 535)	82.8 % (264 of 319)	90.9 % (10 of 11)
Aromatic	65.0 % (52 of 80)	82.5 % (33 of 40)	47.5 % (19 of 40)
Methyl	96.7 % (118 of 122)	98.4 % (60 of 61)	95.1 % (58 of 61)

1. PDZ2

GIDPFTMLRP RLCTMKKGPS GYGFNLHSDK SKPGQFIRSV DPDSPAEASG LRAQDRIVEV NGVCMEGKQH GDVVSAIRAG GDETKLLVVD RETDEFFKKC RVIPSQEHLN GPLPVPFTNG EIQKENSR

2. CFTR

QDTRL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
9	PDZ2	[U-99% 13C; U-99% 15N]		200 uM
10	TRIS	natural abundance		20 mM
11	sodium chloride	natural abundance		150 mM
12	DTT	natural abundance		0.5 mM
13	EDTA	natural abundance		0.5 mM
14	CFTR	natural abundance		275 uM
15	H2O	natural abundance		90 %
16	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M0V, Strand ID: A, B Detail

Release date

2013-04-21

Citation

Ligand-induced dynamic changes in extended PDZ domains from NHERF1
Bhattacharya, S., Ju, J., Orlova, N., Khajeh, J., Cowburn, D., Bu, Z.
J. Mol. Biol. (2013), 425, 2509-2528, PubMed 23583913 , DOI 10.1016/j.jmb.2013.04.001 , Abstract

Related entities 1. PDZ2, : 1 : 33 entities Detail

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

5 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

6 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

7 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

8 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

9 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

10 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

11 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

12 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

13 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
9	PDZ2	[U-99% 13C; U-99% 15N]		200 uM
10	TRIS	natural abundance		20 mM
11	sodium chloride	natural abundance		150 mM
12	DTT	natural abundance		0.5 mM
13	EDTA	natural abundance		0.5 mM
14	CFTR	natural abundance		275 uM
15	H2O	natural abundance		90 %
16	D2O	natural abundance		10 %

14 2D 13C,15N f1,f2-filtered TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

15 2D 13C,15N f1,f2-filtered NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

16 2D 13C,15N f2-filtered NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

17 3D 13C,15N f1-filtered 13C-edited NOESY-HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

18 3D 13C,15N f1-filtered 15N-edited NOESY-HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	CFTR	natural abundance		688 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18826_2m0v.nef
Input source #2: Coordindates	2m0v.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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	272	.	Not matched with CCD	None
B	273	.	Not matched with CCD	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-----150-------160-------170-------180-------190-------200-------210-------220-------230-------240--
GIDPFTMLRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDRETDEFFKKC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GIDPFTMLRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDRETDEFFKKC
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----250-------260-------270
RVIPSQEHLNGPLPVPFTNGEIQKENSR
||||||||||||||||||||||||||||
RVIPSQEHLNGPLPVPFTNGEIQKENSR
-------110-------120--------

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

---- 
Q..R 
|  | 
QDTRL
-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	128	0	0	100.0
B	B	5	4	0	100.0

Content subtype: combined_18826_2m0v.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1397		100.0 (chain: A, length: 128)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2733 (1)	noe	99.2 (chain: A, length: 128), 44.4 (chain: B, length: 9)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	124 (124)	.	60.9 (chain: A, length: 128)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 100.0%

-----150-------160-------170-------180-------190-------200-------210-------220-------230-------240--
GIDPFTMLRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDRETDEFFKKC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GIDPFTMLRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDRETDEFFKKC

-----250-------260-------270
RVIPSQEHLNGPLPVPFTNGEIQKENSR
||||||||||||||||||||||||||||
RVIPSQEHLNGPLPVPFTNGEIQKENSR

Total number of assignments
- ¹H chemical shifts: 757
- ¹³C chemical shifts: 508
- ¹⁵N chemical shifts: 132

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
151	ARG	HH11	6.328
151	ARG	HH12	6.328
186	SER	HG	6.456
191	SER	HG	5.009
194	ARG	HH12	6.839
194	ARG	HH11	6.355
220	ARG	HH11	6.51
220	ARG	HH12	6.51
226	THR	HG1	4.095
233	ARG	HH11	6.337
233	ARG	HH12	6.883
235	THR	HG1	6.087
243	ARG	HH11	6.146
243	ARG	HH12	6.46

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	772	735	95.2
¹³C chemical shifts	563	508	90.2
¹⁵N chemical shifts	137	132	96.4

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	259	255	98.5
¹³C chemical shifts	256	241	94.1
¹⁵N chemical shifts	118	117	99.2

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	513	480	93.6
¹³C chemical shifts	307	267	87.0
¹⁵N chemical shifts	19	15	78.9

Methyl group atoms

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

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	33	82.5
¹³C chemical shifts	40	19	47.5

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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 99.2%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 44.4%
- Total number of restraints: 2733
- Weight of restraints: 1.0 (2733)
- Potential type of restraints: square-well-parabolic (2733)
- Range of distance target values: 2.08, 4.16 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 128, Sequence coverage: 60.9%
- Total number of restraints: 124
- Total number of restraints per polymer type: 124
- Weight of restraints: 1.0 (124)
- Potential type of restraints: square-well-parabolic (124)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PDZ domain, Protein/Peptide