BMRBj - BMREntryMaster

Found 1 Document (0.845 seconds)

BMRB: 18825

2M0U

Complex structure of C-terminal CFTR peptide and extended PDZ1 domain from NHERF1.

Authors

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

Assembly

C-terminal CFTR peptide and extended PDZ1 domain from NHERF1

Entity

1. PDZ1 (polymer, Thiol state: all free), 117 monomers, 12805.47 Da Detail

GIDPFTMLPR LCCLEKGPNG YGFHLHGEKG KLGQYIRLVE PGSPAEKAGL LAGDRLVEVN GENVEKETHQ QVVSRIRAAL NAVRLLVVDP ETDEQLQKLG VQVREELLRA QEAPGQA

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

QDTRL

Total weight

13437.148 Da

Max. entity weight

12805.47 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.5 %, Completeness: 88.6 %, Completeness (bb): 89.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.6 % (1241 of 1401)	88.9 % (654 of 736)	87.9 % (472 of 537)	89.8 % (115 of 128)
Backbone	89.6 % (643 of 718)	91.2 % (228 of 250)	88.4 % (312 of 353)	89.6 % (103 of 115)
Sidechain	88.0 % (697 of 792)	87.7 % (426 of 486)	88.4 % (259 of 293)	92.3 % (12 of 13)
Aromatic	95.8 % (46 of 48)	100.0 % (24 of 24)	91.7 % (22 of 24)
Methyl	95.3 % (143 of 150)	97.3 % (73 of 75)	93.3 % (70 of 75)

1. PDZ1

GIDPFTMLPR LCCLEKGPNG YGFHLHGEKG KLGQYIRLVE PGSPAEKAGL LAGDRLVEVN GENVEKETHQ QVVSRIRAAL NAVRLLVVDP ETDEQLQKLG VQVREELLRA QEAPGQA

2. CFTR

QDTRL

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M0U, 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. PDZ1, : 1 : 52 entities Detail

Experiments performed 16 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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

10 3D HNCACB

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
1	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

11 3D HNCO

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
1	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

12 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
1	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

13 4D 13C,15N NOESY

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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

14 4D 13C,13C NOESY aliphatic

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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 uM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

15 2D 13C,15N f1,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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 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	PDZ1	[U-99% 13C; U-99% 15N]		286 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		275 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_18825_2m0u.nef
Input source #2: Coordindates	2m0u.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---
GIDPFTMLPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQLQKLG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GIDPFTMLPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQLQKLG
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----110-------120
VQVREELLRAQEAPGQA
|||||||||||||||||
VQVREELLRAQEAPGQA
-------110-------

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

-----
QDTRL
|||||
QDTRL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	117	0	0	100.0
B	B	5	0	0	100.0

Content subtype: combined_18825_2m0u.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1279		98.3 (chain: A, length: 117), 100.0 (chain: B, length: 5)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2542 (1)	noe	97.4 (chain: A, length: 117), 80.0 (chain: B, length: 5)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	118 (118)	.	70.1 (chain: A, length: 117)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 98.3%
  - Entity_assembly_ID: B, Chain length: 5, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 682
  - ¹³C chemical shifts: 481
  - ¹⁵N chemical shifts: 116
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 97.4%
  - Entity_assembly_ID: B, Chain length: 5, Sequence coverage: 80.0%
- Total number of restraints: 2542
- Weight of restraints: 1.0 (2542)
- Potential type of restraints: square-well-parabolic (2542)
- Range of distance target values: 2.04, 3.84 (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: 117, Sequence coverage: 70.1%
- Total number of restraints: 118
- Total number of restraints per polymer type: 118
- Weight of restraints: 1.0 (118)
- Potential type of restraints: square-well-parabolic (118)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PDZ domain, Protein/Peptide