BMRBj - BMREntryMaster

Found 1 Document (0.749 seconds)

BMRB: 34160

5OEK

Putative active dimeric state of GHR transmembrane domain

Authors

Lesovoy, D.M., Bocharov, E.V., Bocharova, O.V., Urban, A.S., Arseniev, A.S.

Assembly

Growth hormone receptor

Entity

1. Growth hormone receptor (polymer), 43 monomers, 5142.102 × 2 Da Detail

GSMSQFTCEE DFYFPWLLII IFGIFGLTVM LFVFLFSKQQ RIK

Total weight

10284.204 Da

Max. entity weight

5142.102 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.8 %, Completeness (bb): 97.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.8 % (562 of 569)	99.7 % (292 of 293)	98.3 % (226 of 230)	95.7 % (44 of 46)
Backbone	97.3 % (249 of 256)	98.9 % (87 of 88)	96.8 % (122 of 126)	95.2 % (40 of 42)
Sidechain	100.0 % (353 of 353)	100.0 % (205 of 205)	100.0 % (144 of 144)	100.0 % (4 of 4)
Aromatic	100.0 % (100 of 100)	100.0 % (50 of 50)	100.0 % (49 of 49)	100.0 % (1 of 1)
Methyl	100.0 % (52 of 52)	100.0 % (26 of 26)	100.0 % (26 of 26)

1. entity 1

GSMSQFTCEE DFYFPWLLII IFGIFGLTVM LFVFLFSKQQ RIK

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.0 (±0.05), Details 0.7 mM [U-99% 13C; U-99% 15N] GHRtm, 1.2 mM GHRtm, 100 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	GHRtm-13C-15N	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	GHRtm	natural abundance	1.2 (±0.2) mM
3	DPC	[U-99% 2H]	100 (±2.0) mM
4	sodium azide	natural abundance	0.3 mM
5	TCEP	natural abundance	8 mM
6	citric acid	natural abundance	10 mM
7	Na2HPO4	natural abundance	20 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.0 (±0.05), Details 0.8 mM [U-99% 15N] GHRtm, 50 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
8	GHRtm	[U-99% 15N]	0.8 (±0.1) mM
9	DPC	[U-99% 2H]	50 (±1.0) mM
10	sodium azide	natural abundance	0.3 mM
11	TCEP	natural abundance	8 mM
12	citric acid	natural abundance	10 mM
13	Na2HPO4	natural abundance	20 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.0 (±0.05), Details 0.8 mM [U-99% 13C; U-99% 15N] GHRtm, 50 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

Protein Blocks Logo

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

Release date

2018-04-03

Citation 1

[Preparation of Transmembrane Fragments Growth Hormone Receptor GHR in a Cell-Free Expression System for Structural Studies]
Bocharova, O.V., Kuzmichev, P.K., Urban, A.S., Goncharuk, S.A., Bocharov, E.V., Arsenyev, A.S.
Bioorg. Khim. (2015), 41, 701-708, PubMed 27125024 , DOI: , Abstract

Show more 1 citaion

Citation 2

Structural basis of the signal transduction via transmembrane domain of the human growth hormone receptor
Bocharov, E.V., Lesovoy, D.M., Bocharova, O.V., Urban, A.S., Pavlov, K.V., Volynsky, P.E., Efremov, R.G., Arseniev, A.S.
Biochim. Biophys. Acta (2018), 1862, 1410-1420, PubMed 29571748 , DOI 10.1016/j.bbagen.2018.03.022 , Abstract

Hide non-primary 1 citaion

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34164 released on 2018-04-03
Title Putative inactive (dormant) dimeric state of GHR transmembrane domain

Related entities 1. Growth hormone receptor, : 1 : 1 : 2 : 21 entities Detail

Interaction partners 1. Growth hormone receptor, : 14 interactors Detail

More details for 14 interactors identified by 5 citations

Experiments performed 22 experiments Detail

1 15N,13C-F1-filtered/F3-edited-NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.0 (±0.05), Details 0.7 mM [U-99% 13C; U-99% 15N] GHRtm, 1.2 mM GHRtm, 100 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	GHRtm-13C-15N	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	GHRtm	natural abundance	1.2 (±0.2) mM
3	DPC	[U-99% 2H]	100 (±2.0) mM
4	sodium azide	natural abundance	0.3 mM
5	TCEP	natural abundance	8 mM
6	citric acid	natural abundance	10 mM
7	Na2HPO4	natural abundance	20 mM

2 15N,13C-F1-filtered/F3-edited-NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.0 (±0.05), Details 0.8 mM [U-99% 13C; U-99% 15N] GHRtm, 50 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

3 3D 1H-13C(constant time) NOESY aliphatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

4 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

5 3D 1H-15N(TROSY) NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.0 (±0.05), Details 0.8 mM [U-99% 15N] GHRtm, 50 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
8	GHRtm	[U-99% 15N]	0.8 (±0.1) mM
9	DPC	[U-99% 2H]	50 (±1.0) mM
10	sodium azide	natural abundance	0.3 mM
11	TCEP	natural abundance	8 mM
12	citric acid	natural abundance	10 mM
13	Na2HPO4	natural abundance	20 mM

6 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

7 3D 1H-15N(TROSY) HNHB

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
8	GHRtm	[U-99% 15N]	0.8 (±0.1) mM
9	DPC	[U-99% 2H]	50 (±1.0) mM
10	sodium azide	natural abundance	0.3 mM
11	TCEP	natural abundance	8 mM
12	citric acid	natural abundance	10 mM
13	Na2HPO4	natural abundance	20 mM

8 3D 1H-15N(TROSY) HNHA

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
8	GHRtm	[U-99% 15N]	0.8 (±0.1) mM
9	DPC	[U-99% 2H]	50 (±1.0) mM
10	sodium azide	natural abundance	0.3 mM
11	TCEP	natural abundance	8 mM
12	citric acid	natural abundance	10 mM
13	Na2HPO4	natural abundance	20 mM

9 3D 1H-15N(TROSY) HNCO

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

10 3D 1H-15N(TROSY) HNCA

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

11 3D 1H-15N(TROSY) HN(CA)CO

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

12 3D 1H-15N(TROSY) HN(CO)CA

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

13 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	GHRtm-13C-15N	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	GHRtm	natural abundance	1.2 (±0.2) mM
3	DPC	[U-99% 2H]	100 (±2.0) mM
4	sodium azide	natural abundance	0.3 mM
5	TCEP	natural abundance	8 mM
6	citric acid	natural abundance	10 mM
7	Na2HPO4	natural abundance	20 mM

14 2D 1H-15N TROSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	GHRtm-13C-15N	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	GHRtm	natural abundance	1.2 (±0.2) mM
3	DPC	[U-99% 2H]	100 (±2.0) mM
4	sodium azide	natural abundance	0.3 mM
5	TCEP	natural abundance	8 mM
6	citric acid	natural abundance	10 mM
7	Na2HPO4	natural abundance	20 mM

15 2D 1H-INEPT-13CA-detected

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

16 2D 1H-13C constant time HSQC aliphatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	GHRtm-13C-15N	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	GHRtm	natural abundance	1.2 (±0.2) mM
3	DPC	[U-99% 2H]	100 (±2.0) mM
4	sodium azide	natural abundance	0.3 mM
5	TCEP	natural abundance	8 mM
6	citric acid	natural abundance	10 mM
7	Na2HPO4	natural abundance	20 mM

17 2D 1H-13C constant time HSQC aromatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	GHRtm-13C-15N	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	GHRtm	natural abundance	1.2 (±0.2) mM
3	DPC	[U-99% 2H]	100 (±2.0) mM
4	sodium azide	natural abundance	0.3 mM
5	TCEP	natural abundance	8 mM
6	citric acid	natural abundance	10 mM
7	Na2HPO4	natural abundance	20 mM

18 2D 1H-13C(TROSY) constant time HSQC aromatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

19 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

20 3D 1H-13C constant time HCCH-TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
14	GHRtm	[U-99% 13C; U-99% 15N]	0.8 (±0.1) mM
15	DPC	[U-99% 2H]	50 (±1.0) mM
16	sodium azide	natural abundance	0.3 mM
17	TCEP	natural abundance	8 mM
18	citric acid	natural abundance	10 mM
19	Na2HPO4	natural abundance	20 mM

21 2D 1H-15N CSA/dipole cross-correlation

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
8	GHRtm	[U-99% 15N]	0.8 (±0.1) mM
9	DPC	[U-99% 2H]	50 (±1.0) mM
10	sodium azide	natural abundance	0.3 mM
11	TCEP	natural abundance	8 mM
12	citric acid	natural abundance	10 mM
13	Na2HPO4	natural abundance	20 mM

22 2D 1H-15N(TROSY) CLEANEX

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
8	GHRtm	[U-99% 15N]	0.8 (±0.1) mM
9	DPC	[U-99% 2H]	50 (±1.0) mM
10	sodium azide	natural abundance	0.3 mM
11	TCEP	natural abundance	8 mM
12	citric acid	natural abundance	10 mM
13	Na2HPO4	natural abundance	20 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34160_5oek.nef
Input source #2: Coordindates	5oek.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

------260-------270-------280-------290----
GSMSQFTCEEDFYFPWLLIIIFGIFGLTVMLFVFLFSKQQRIK
|||||||||||||||||||||||||||||||||||||||||||
GSMSQFTCEEDFYFPWLLIIIFGIFGLTVMLFVFLFSKQQRIK
--------10--------20--------30--------40---

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

------260-------270-------280-------290----
GSMSQFTCEEDFYFPWLLIIIFGIFGLTVMLFVFLFSKQQRIK
|||||||||||||||||||||||||||||||||||||||||||
GSMSQFTCEEDFYFPWLLIIIFGIFGLTVMLFVFLFSKQQRIK
--------10--------20--------30--------40---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	43	0	0	100.0
B	B	43	0	0	100.0

Content subtype: combined_34160_5oek.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	568		100.0 (chain: A, length: 43)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	32 (1)	noe	14.0 (chain: A, length: 43), 14.0 (chain: B, length: 43)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 43, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 297
  - ¹³C chemical shifts: 226
  - ¹⁵N chemical shifts: 45
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
253	SER	HG	4.133
255	SER	HG	4.712
258	THR	HG1	4.449
279	THR	HG1	4.0
288	SER	HG	4.574

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	293	292	99.7
¹³C chemical shifts	230	226	98.3
¹⁵N chemical shifts	47	45	95.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	87	98.9
¹³C chemical shifts	86	82	95.3
¹⁵N chemical shifts	42	40	95.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	205	205	100.0
¹³C chemical shifts	144	144	100.0
¹⁵N chemical shifts	5	5	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	28	100.0
¹³C chemical shifts	28	28	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	50	100.0
¹³C chemical shifts	49	49	100.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 43, Sequence coverage: 14.0%
  - Entity_assembly_ID: B, Chain length: 43, Sequence coverage: 14.0%
- Total number of restraints: 32
- Weight of restraints: 1.0 (32)
- Potential type of restraints: upper-bound-parabolic (32)
- Range of distance target values: 0.0, 4.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords Dimer, GHR, Growth hormone receptor, Homodimer, Human, MEMBRANE PROTEIN, Receptor, Transmembrane domain, Tyrosine kinase

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.749 seconds)

BMRB: 34160

Sample #1

Sample #2

Sample #3

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Growth hormone receptor, : 1 : 1 : 2 : 21 entities Detail

Interaction partners 1. Growth hormone receptor, : 14 interactors Detail

Experiments performed 22 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail