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BMRB: 17752

2LFG

SOLUTION STRUCTURE OF THE HUMAN PROLACTIN RECEPTOR ECD DOMAIN D2

Authors

Dagil, R., Knudsen, M.J., Kragelund, B.B., O'Shea, C.

Assembly

hPRLR-D2

Entity

1. hPRLR-D2 (polymer, Thiol state: all free), 113 monomers, 13328.22 Da Detail

MYIVQPDPPL ELAVEVKQPE DRKPYLWIKW SPPTLIDLKT GWFTLLYEIR LKPEKAAEWE IHFAGQQTEF KILSLHPGQK YLVQVRCKPD HGYWSAWSPA TFIQIPSDFT MND

Formula weight

13328.22 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.8 %, Completeness (bb): 97.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.8 % (1340 of 1428)	91.3 % (683 of 748)	96.6 % (546 of 565)	96.5 % (111 of 115)
Backbone	97.2 % (636 of 654)	97.2 % (212 of 218)	97.3 % (326 of 335)	97.0 % (98 of 101)
Sidechain	92.0 % (812 of 883)	88.9 % (471 of 530)	96.8 % (328 of 339)	92.9 % (13 of 14)
Aromatic	94.3 % (164 of 174)	96.6 % (84 of 87)	91.4 % (74 of 81)	100.0 % (6 of 6)
Methyl	100.0 % (120 of 120)	100.0 % (60 of 60)	100.0 % (60 of 60)

1. hPRLR-D2

MYIVQPDPPL ELAVEVKQPE DRKPYLWIKW SPPTLIDLKT GWFTLLYEIR LKPEKAAEWE IHFAGQQTEF KILSLHPGQK YLVQVRCKPD HGYWSAWSPA TFIQIPSDFT MND

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
8	hPRLR-D2	[U-100% 13C(1)]		0.5 mM
9	sodium phosphate	natural abundance		10 mM
10	TCEP	natural abundance		10 mM
11	sodium azide	natural abundance		0.02 %
12	DSS	natural abundance		1 mM
13	D2O	natural abundance		100 %

LACS Plot; CA

Referencing offset: -0.07 ppm, Outliers: 4 Detail

LACS Plot; CB

Referencing offset: -0.07 ppm, Outliers: 4 Detail

LACS Plot; HA

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.84 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-02-12

Citation

The WSXWS motif in cytokine receptors is a molecular switch involved in receptor activation: insight from structures of the prolactin receptor
Dagil, R., Knudsen, M.J., Olsen, J.G., O'Shea, C., Franzmann, M., Goffin, V., Teilum, K., Breinholt, J., Kragelund, B.B.
Structure (2012), 20, 270-282, PubMed 22325776 , DOI 10.1016/j.str.2011.12.010 , Abstract

Related entities 1. hPRLR-D2, : 1 : 12 : 151 entities Detail

Interaction partners 1. hPRLR-D2, : 5 interactors Detail

More details for 5 interactors identified by 4 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

3 3D C(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

4 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

5 3D HNCA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

6 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

7 3D HN(CO)CA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

8 3D H(CCO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

9 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

10 3D HN(CA)CO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

12 3D 1H-15N TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

13 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

14 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

15 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	hPRLR-D2	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		10 mM
3	TCEP	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

16 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
8	hPRLR-D2	[U-100% 13C(1)]		0.5 mM
9	sodium phosphate	natural abundance		10 mM
10	TCEP	natural abundance		10 mM
11	sodium azide	natural abundance		0.02 %
12	DSS	natural abundance		1 mM
13	D2O	natural abundance		100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17752_2lfg.nef
Input source #2: Coordindates	2lfg.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

--100-----110-------120-------130-------140-------150-------160-------170-------180-------190-------
MYIVQPDPPLELAVEVKQPEDRKPYLWIKWSPPTLIDLKTGWFTLLYEIRLKPEKAAEWEIHFAGQQTEFKILSLHPGQKYLVQVRCKPDHGYWSAWSPA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MYIVQPDPPLELAVEVKQPEDRKPYLWIKWSPPTLIDLKTGWFTLLYEIRLKPEKAAEWEIHFAGQQTEFKILSLHPGQKYLVQVRCKPDHGYWSAWSPA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

200-------210
TFIQIPSDFTMND
|||||||||||||
TFIQIPSDFTMND
-------110---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	113	0	0	100.0

Content subtype: combined_17752_2lfg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1350		100.0 (chain: A, length: 113)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3922 (1)	noe	99.1 (chain: A, length: 113)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	105 (105)	.	67.3 (chain: A, length: 113)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 689
  - ¹³C chemical shifts: 549
  - ¹⁵N chemical shifts: 112
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 99.1%
- Total number of restraints: 3791
- Weight of restraints: 1.0 (3791)
- Potential type of restraints: square-well-parabolic (3791)
- Range of distance target values: 2.04, 4.9 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 67.3%
- Total number of restraints: 105
- Total number of restraints per polymer type: 105
- Weight of restraints: 1.0 (105)
- Potential type of restraints: square-well-parabolic (105)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Cytokine receptor, D2 domain, Extracellular domain, Fibronectin type III, Hormone receptor, Prolactin receptor, WSXWS