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BMRB: 25729

2N5S

Spatial structure of EGFR transmembrane and juxtamembrane domains in DPC micelles

Authors

Mineev, K., Bocharov, E., Bocharova, O., Arseniev, A.

Assembly

EGFR transmembrane and juxtamembrane domains

Entity

1. EGFR transmembrane and juxtamembrane domains (polymer), 54 monomers, 5968.254 Da Detail

GSCKIPSIAT GMVGALLLLL VVALGIGLFM RRRHIVRKRT LRRLLQEREL VEGG

Formula weight

5968.254 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.6 %, Completeness (bb): 98.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.6 % (630 of 639)	98.5 % (329 of 334)	98.8 % (248 of 251)	98.1 % (53 of 54)
Backbone	98.4 % (317 of 322)	97.4 % (111 of 114)	99.4 % (154 of 155)	98.1 % (52 of 53)
Sidechain	98.9 % (360 of 364)	99.1 % (218 of 220)	98.6 % (141 of 143)	100.0 % (1 of 1)
Aromatic	85.7 % (12 of 14)	100.0 % (7 of 7)	71.4 % (5 of 7)
Methyl	100.0 % (90 of 90)	100.0 % (45 of 45)	100.0 % (45 of 45)

1. EGFR

GSCKIPSIAT GMVGALLLLL VVALGIGLFM RRRHIVRKRT LRRLLQEREL VEGG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 314 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	EGFR	[U-100% 13C; U-100% 15N]		0.3 mM
2	TCEP	natural abundance		2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2N5S, Strand ID: A Detail

Release date

2015-10-11

Citation

The Membrane Mimetic Affects the Spatial Structure and Mobility of EGFR Transmembrane and Juxtamembrane Domains
Mineev, K., Panova, S.V., Bocharov, E., Bocharov, O., Arseniev, A.
Biochemistry (2015), 54, 6295-6298, PubMed 26440883 , DOI 10.1021/acs.biochem.5b00851 , Abstract

Related entities 1. EGFR transmembrane and juxtamembrane domains, : 1 : 3 : 32 entities Detail

Interaction partners 1. EGFR transmembrane and juxtamembrane domains, : 293 interactors Detail

More details for 293 interactors identified by 80 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 314 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	EGFR	[U-100% 13C; U-100% 15N]		0.3 mM
2	TCEP	natural abundance		2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 314 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	EGFR	[U-100% 13C; U-100% 15N]		0.3 mM
2	TCEP	natural abundance		2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 314 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	EGFR	[U-100% 13C; U-100% 15N]		0.3 mM
2	TCEP	natural abundance		2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 314 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	EGFR	[U-100% 13C; U-100% 15N]		0.3 mM
2	TCEP	natural abundance		2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 314 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	EGFR	[U-100% 13C; U-100% 15N]		0.3 mM
2	TCEP	natural abundance		2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 314 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	EGFR	[U-100% 13C; U-100% 15N]		0.3 mM
2	TCEP	natural abundance		2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 314 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	EGFR	[U-100% 13C; U-100% 15N]		0.3 mM
2	TCEP	natural abundance		2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 314 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	EGFR	[U-100% 13C; U-100% 15N]		0.3 mM
2	TCEP	natural abundance		2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 HSQC-NOESY-HSQC CN

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 314 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	EGFR	[U-100% 13C; U-100% 15N]		0.3 mM
2	TCEP	natural abundance		2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	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_25729_2n5s.nef
Input source #2: Coordindates	2n5s.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

-40-------50--------60--------70--------80--------90--
GSCKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKRTLRRLLQERELVEGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSCKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKRTLRRLLQERELVEGG
--------10--------20--------30--------40--------50----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	54	0	0	100.0

Content subtype: combined_25729_2n5s.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	630		98.1 (chain: A, length: 54)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	345 (1)	noe	94.4 (chain: A, length: 54)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	121 (121)	.	85.2 (chain: A, length: 54)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 98.1%
- Total number of assignments
  - ¹H chemical shifts: 327
  - ¹³C chemical shifts: 246
  - ¹⁵N chemical shifts: 57
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 94.4%
- Total number of restraints: 345
- Weight of restraints: 1.0 (345)
- Potential type of restraints: upper-bound-parabolic (345)
- Range of distance target values: 2.55, 4.91 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 85.2%
- Total number of restraints: 121
- Total number of restraints per polymer type: 121
- Weight of restraints: 1.0 (121)
- Potential type of restraints: square-well-parabolic (121)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords EGFR, ErbB1, HER1, micelles, transmembrane