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BMRB: 36064

5X9X

Solution structure of heterodimeric coiled-coil domain of Drosophila GABAB receptor 1 and 2

Authors

Liu, X., Zhang, S., Liu, J., Zhang, C.X.

Assembly

Metabotropic GABA-B receptor subtype 1, Metabotropic GABA-B receptor subtype 2

Entity

1. Metabotropic GABA-B receptor subtype 1 (polymer, Thiol state: not present), 44 monomers, 5402.017 Da Detail

MDSKEDEERY QKLVTENEQL QRLITQKEEK IRVLRQRLVE RGDA

2. Metabotropic GABA-B receptor subtype 2 (polymer, Thiol state: not present), 45 monomers, 5138.814 Da Detail

GPLGSSVSEL EQRLRDVKNT NSRFRKALME KENELQALIR KLGPE

Total weight

10540.831 Da

Max. entity weight

5402.017 Da

Source organism

Drosophila melanogaster

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.8 %, Completeness: 87.3 %, Completeness (bb): 92.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.3 % (952 of 1090)	85.7 % (503 of 587)	87.7 % (355 of 405)	95.9 % (94 of 98)
Backbone	92.8 % (492 of 530)	94.4 % (170 of 180)	90.5 % (238 of 263)	96.6 % (84 of 87)
Sidechain	84.2 % (543 of 645)	81.8 % (333 of 407)	88.1 % (200 of 227)	90.9 % (10 of 11)
Aromatic	50.0 % (9 of 18)	100.0 % (9 of 9)	0.0 % (0 of 9)
Methyl	95.7 % (88 of 92)	95.7 % (44 of 46)	95.7 % (44 of 46)

1. Metabotropic GABA-B receptor subtype 1

MDSKEDEERY QKLVTENEQL QRLITQKEEK IRVLRQRLVE RGDA

2. Metabotropic GABA-B receptor subtype 2

GPLGSSVSEL EQRLRDVKNT NSRFRKALME KENELQALIR KLGPE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0, Details 20 mM PBS, 100 mM NaCl, 0.02 mg/mL NaN3, 0.8 mM [U-99% 15N] coiled-coil domain of Drosophila GABAB receptor 1, 0.8 mM [U-99% 15N] coiled-coil domain of Drosophila GABAB receptor 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	NaCl	natural abundance	salt	100 mM
2	NaN3	natural abundance		0.02 mg/mL
3	PBS	natural abundance	buffer	20 mM
4	coiled-coil domain of Drosophila GABAB receptor 1	[U-99% 15N]	protein	0.8 mM
5	coiled-coil domain of Drosophila GABAB receptor 2	[U-99% 15N]	protein	0.8 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0, Details 20 mM PBS, 100 mM NaCl, 0.02 mg/mL NaN3, 0.7 mM [U-13C; U-15N] coiled-coil domain of Drosophila GABAB receptor 1, 0.7 mM [U-13C; U-15N] coiled-coil domain of Drosophila GABAB receptor 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
8	NaCl	natural abundance	salt	100 mM
9	NaN3	natural abundance		0.02 mg/mL
10	PBS	natural abundance	buffer	20 mM
11	coiled-coil domain of Drosophila GABAB receptor 1	[U-13C; U-15N]	protein	0.7 mM
12	coiled-coil domain of Drosophila GABAB receptor 2	[U-13C; U-15N]	protein	0.7 mM
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 5X9X, Strand ID: A, B Detail

Release date

2017-06-03

Citation

Solution structure of heterodimeric coiled-coil domain of Drosophila GABAB receptor 1 and 2
Liu, X., Zhang, S.

Related entities 1. Metabotropic GABA-B receptor subtype 1, : 1 : 1 : 32 entities Detail

Related entities 2. Metabotropic GABA-B receptor subtype 2, : 1 : 16 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent DD2 600 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0, Details 20 mM PBS, 100 mM NaCl, 0.02 mg/mL NaN3, 0.8 mM [U-99% 15N] coiled-coil domain of Drosophila GABAB receptor 1, 0.8 mM [U-99% 15N] coiled-coil domain of Drosophila GABAB receptor 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	NaCl	natural abundance	salt	100 mM
2	NaN3	natural abundance		0.02 mg/mL
3	PBS	natural abundance	buffer	20 mM
4	coiled-coil domain of Drosophila GABAB receptor 1	[U-99% 15N]	protein	0.8 mM
5	coiled-coil domain of Drosophila GABAB receptor 2	[U-99% 15N]	protein	0.8 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

2 2D 1H-15N HSQC

Instrument

Agilent DD2 600 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0, Details 20 mM PBS, 100 mM NaCl, 0.02 mg/mL NaN3, 0.7 mM [U-13C; U-15N] coiled-coil domain of Drosophila GABAB receptor 1, 0.7 mM [U-13C; U-15N] coiled-coil domain of Drosophila GABAB receptor 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
8	NaCl	natural abundance	salt	100 mM
9	NaN3	natural abundance		0.02 mg/mL
10	PBS	natural abundance	buffer	20 mM
11	coiled-coil domain of Drosophila GABAB receptor 1	[U-13C; U-15N]	protein	0.7 mM
12	coiled-coil domain of Drosophila GABAB receptor 2	[U-13C; U-15N]	protein	0.7 mM
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

3 2D 1H-13C HSQC aliphatic

Instrument

Agilent DD2 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
8	NaCl	natural abundance	salt	100 mM
9	NaN3	natural abundance		0.02 mg/mL
10	PBS	natural abundance	buffer	20 mM
11	coiled-coil domain of Drosophila GABAB receptor 1	[U-13C; U-15N]	protein	0.7 mM
12	coiled-coil domain of Drosophila GABAB receptor 2	[U-13C; U-15N]	protein	0.7 mM
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

4 3D CBCA(CO)NH

Instrument

Agilent DD2 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
8	NaCl	natural abundance	salt	100 mM
9	NaN3	natural abundance		0.02 mg/mL
10	PBS	natural abundance	buffer	20 mM
11	coiled-coil domain of Drosophila GABAB receptor 1	[U-13C; U-15N]	protein	0.7 mM
12	coiled-coil domain of Drosophila GABAB receptor 2	[U-13C; U-15N]	protein	0.7 mM
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

5 3D HNCACB

Instrument

Agilent DD2 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
8	NaCl	natural abundance	salt	100 mM
9	NaN3	natural abundance		0.02 mg/mL
10	PBS	natural abundance	buffer	20 mM
11	coiled-coil domain of Drosophila GABAB receptor 1	[U-13C; U-15N]	protein	0.7 mM
12	coiled-coil domain of Drosophila GABAB receptor 2	[U-13C; U-15N]	protein	0.7 mM
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

6 3D HBHA(CO)NH

Instrument

Agilent DD2 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
8	NaCl	natural abundance	salt	100 mM
9	NaN3	natural abundance		0.02 mg/mL
10	PBS	natural abundance	buffer	20 mM
11	coiled-coil domain of Drosophila GABAB receptor 1	[U-13C; U-15N]	protein	0.7 mM
12	coiled-coil domain of Drosophila GABAB receptor 2	[U-13C; U-15N]	protein	0.7 mM
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

7 3D 1H-15N NOESY

Instrument

Agilent DD2 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	NaCl	natural abundance	salt	100 mM
2	NaN3	natural abundance		0.02 mg/mL
3	PBS	natural abundance	buffer	20 mM
4	coiled-coil domain of Drosophila GABAB receptor 1	[U-99% 15N]	protein	0.8 mM
5	coiled-coil domain of Drosophila GABAB receptor 2	[U-99% 15N]	protein	0.8 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

8 3D 1H-13C NOESY

Instrument

Agilent DD2 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
8	NaCl	natural abundance	salt	100 mM
9	NaN3	natural abundance		0.02 mg/mL
10	PBS	natural abundance	buffer	20 mM
11	coiled-coil domain of Drosophila GABAB receptor 1	[U-13C; U-15N]	protein	0.7 mM
12	coiled-coil domain of Drosophila GABAB receptor 2	[U-13C; U-15N]	protein	0.7 mM
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

9 3D CCH-TOCSY

Instrument

Agilent DD2 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
8	NaCl	natural abundance	salt	100 mM
9	NaN3	natural abundance		0.02 mg/mL
10	PBS	natural abundance	buffer	20 mM
11	coiled-coil domain of Drosophila GABAB receptor 1	[U-13C; U-15N]	protein	0.7 mM
12	coiled-coil domain of Drosophila GABAB receptor 2	[U-13C; U-15N]	protein	0.7 mM
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

10 3D HCCH-TOCSY

Instrument

Agilent DD2 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
8	NaCl	natural abundance	salt	100 mM
9	NaN3	natural abundance		0.02 mg/mL
10	PBS	natural abundance	buffer	20 mM
11	coiled-coil domain of Drosophila GABAB receptor 1	[U-13C; U-15N]	protein	0.7 mM
12	coiled-coil domain of Drosophila GABAB receptor 2	[U-13C; U-15N]	protein	0.7 mM
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

11 3D HNCO

Instrument

Agilent DD2 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
8	NaCl	natural abundance	salt	100 mM
9	NaN3	natural abundance		0.02 mg/mL
10	PBS	natural abundance	buffer	20 mM
11	coiled-coil domain of Drosophila GABAB receptor 1	[U-13C; U-15N]	protein	0.7 mM
12	coiled-coil domain of Drosophila GABAB receptor 2	[U-13C; U-15N]	protein	0.7 mM
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_36064_5x9x.nef
Input source #2: Coordindates	5x9x.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----
MDSKEDEERYQKLVTENEQLQRLITQKEEKIRVLRQRLVERGDA
||||||||||||||||||||||||||||||||||||||||||||
MDSKEDEERYQKLVTENEQLQRLITQKEEKIRVLRQRLVERGDA

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

---100-------110-------120-------130---------
GPLGSSVSELEQRLRDVKNTNSRFRKALMEKENELQALIRKLGPE
|||||||||||||||||||||||||||||||||||||||||||||
GPLGSSVSELEQRLRDVKNTNSRFRKALMEKENELQALIRKLGPE
--------10--------20--------30--------40-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	44	0	0	100.0
B	B	45	0	0	100.0

Content subtype: combined_36064_5x9x.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	937		97.7 (chain: A, length: 44), 97.8 (chain: B, length: 45)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1275 (1)	noe	97.7 (chain: A, length: 44), 95.6 (chain: B, length: 45)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	63 (1)	hbond	84.1 (chain: A, length: 44), 75.6 (chain: B, length: 45)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	145 (145)	.	88.6 (chain: A, length: 44), 80.0 (chain: B, length: 45)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 97.7%
  - Entity_assembly_ID: B, Chain length: 45, Sequence coverage: 97.8%
- Total number of assignments
  - ¹H chemical shifts: 497
  - ¹³C chemical shifts: 346
  - ¹⁵N chemical shifts: 94
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Peptide bond of PRO
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	297	252	84.8
¹³C chemical shifts	203	170	83.7
¹⁵N chemical shifts	56	47	83.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	85	95.5
¹³C chemical shifts	88	70	79.5
¹⁵N chemical shifts	44	42	95.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	208	167	80.3
¹³C chemical shifts	115	100	87.0
¹⁵N chemical shifts	12	5	41.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	23	95.8
¹³C chemical shifts	24	23	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	290	245	84.5
¹³C chemical shifts	202	176	87.1
¹⁵N chemical shifts	53	47	88.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	91	87	95.6
¹³C chemical shifts	90	78	86.7
¹⁵N chemical shifts	43	42	97.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	199	158	79.4
¹³C chemical shifts	112	98	87.5
¹⁵N chemical shifts	10	5	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	21	87.5
¹³C chemical shifts	24	21	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0
¹³C chemical shifts	5	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 97.7%
  - Entity_assembly_ID: B, Chain length: 45, Sequence coverage: 95.6%
- Total number of restraints: 1275
- Weight of restraints: 1.0 (1275)
- Potential type of restraints: square-well-parabolic (1275)
- Range of distance target values: 1.44, 4.77 (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
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 84.1%
    - Entity_assembly_ID: B, Chain length: 45, Sequence coverage: 75.6%
  - Total number of restraints: 63
  - Weight of restraints: 1.0 (63)
  - Potential type of restraints: square-well-parabolic (63)
  - Range of distance target values: 2.21, 2.21 (Å)
  - 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: 44, Sequence coverage: 88.6%
  - Entity_assembly_ID: B, Chain length: 45, Sequence coverage: 80.0%
- Total number of restraints: 145
- Total number of restraints per polymer type: 145
- Weight of restraints: 1.0 (145)
- Potential type of restraints: square-well-parabolic (145)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords Drosophila, GABAB receptor, SIGNALING PROTEIN, coiled-coil

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Found 1 Document (0.86 seconds)

BMRB: 36064

Sample #1

Sample #2

Related entities 1. Metabotropic GABA-B receptor subtype 1, : 1 : 1 : 32 entities Detail

Related entities 2. Metabotropic GABA-B receptor subtype 2, : 1 : 16 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 5 contents Detail