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BMRB: 34040

5LV6

N-terminal motif dimerization of EGFR transmembrane domain in bicellar environment

Authors

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

Assembly

Epidermal growth factor receptor (E.C.2.7.10.1)

Entity

1. Epidermal growth factor receptor (E.C.2.7.10.1) (polymer), 44 monomers, 4725.781 × 2 Da Detail

EGCPTNGPKI PSIATGMVGA LLLLLVVALG IGLFMRRRHI VRKR

Total weight

9451.562 Da

Max. entity weight

4725.781 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.9 %, Completeness (bb): 96.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.9 % (486 of 512)	94.4 % (252 of 267)	95.1 % (193 of 203)	97.6 % (41 of 42)
Backbone	96.9 % (250 of 258)	96.7 % (88 of 91)	96.0 % (121 of 126)	100.0 % (41 of 41)
Sidechain	93.5 % (273 of 292)	93.2 % (164 of 176)	94.8 % (109 of 115)	0.0 % (0 of 1)
Aromatic	85.7 % (12 of 14)	100.0 % (7 of 7)	71.4 % (5 of 7)
Methyl	94.3 % (66 of 70)	94.3 % (33 of 35)	94.3 % (33 of 35)

1. entity 1

EGCPTNGPKI PSIATGMVGA LLLLLVVALG IGLFMRRRHI VRKR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.8, Details 0.01 % sodium azide, 50 mM phosphate buffer pH 5.8, 5 mM TCEP, 30 mM U-2H DHPC, 10 mM U-2H DMPC, 90% H2O/10% D2O.

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	DHPC	[U-2H]		30 mM
3	DMPC	[U-2H]		10 mM
4	TCEP	natural abundance		5 mM
5	phosphate buffer pH 5.8	natural abundance		50 mM
6	sodium azide	natural abundance		0.01 %

Protein Blocks Logo

Calculated from 20 models in PDB: 5LV6, Strand ID: A, B Detail

Release date

2017-03-26

Citation

The Conformation of the Epidermal Growth Factor Receptor Transmembrane Domain Dimer Dynamically Adapts to the Local Membrane Environment
Bocharov, E.V., Bragin, P.E., Pavlov, K.V., Bocharova, O.V., Mineev, K.S., Polyansky, A.A., Volynsky, P.E., Efremov, R.G., Arseniev, A.S.
Biochemistry (2017), 56, 1697-1705, PubMed 28291355 , DOI 10.1021/acs.biochem.6b01085 , Abstract

Related entities 1. Epidermal growth factor receptor (E.C.2.7.10.1), : 1 : 4 : 2 : 25 entities Detail

Interaction partners 1. Epidermal growth factor receptor (E.C.2.7.10.1), : 293 interactors Detail

More details for 293 interactors identified by 80 citations

Experiments performed 8 experiments Detail

1 3D 1H-13C NOESY with heteronuclear filtration

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.8, Details 0.01 % sodium azide, 50 mM phosphate buffer pH 5.8, 5 mM TCEP, 30 mM U-2H DHPC, 10 mM U-2H DMPC, 90% H2O/10% D2O.

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	DHPC	[U-2H]		30 mM
3	DMPC	[U-2H]		10 mM
4	TCEP	natural abundance		5 mM
5	phosphate buffer pH 5.8	natural abundance		50 mM
6	sodium azide	natural abundance		0.01 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.8, Details 0.01 % sodium azide, 50 mM phosphate buffer pH 5.8, 5 mM TCEP, 30 mM U-2H DHPC, 10 mM U-2H DMPC, 90% H2O/10% D2O.

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	DHPC	[U-2H]		30 mM
3	DMPC	[U-2H]		10 mM
4	TCEP	natural abundance		5 mM
5	phosphate buffer pH 5.8	natural abundance		50 mM
6	sodium azide	natural abundance		0.01 %

3 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.8, Details 0.01 % sodium azide, 50 mM phosphate buffer pH 5.8, 5 mM TCEP, 30 mM U-2H DHPC, 10 mM U-2H DMPC, 90% H2O/10% D2O.

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	DHPC	[U-2H]		30 mM
3	DMPC	[U-2H]		10 mM
4	TCEP	natural abundance		5 mM
5	phosphate buffer pH 5.8	natural abundance		50 mM
6	sodium azide	natural abundance		0.01 %

4 3D HNCO

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.8, Details 0.01 % sodium azide, 50 mM phosphate buffer pH 5.8, 5 mM TCEP, 30 mM U-2H DHPC, 10 mM U-2H DMPC, 90% H2O/10% D2O.

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	DHPC	[U-2H]		30 mM
3	DMPC	[U-2H]		10 mM
4	TCEP	natural abundance		5 mM
5	phosphate buffer pH 5.8	natural abundance		50 mM
6	sodium azide	natural abundance		0.01 %

5 3D HNCA

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.8, Details 0.01 % sodium azide, 50 mM phosphate buffer pH 5.8, 5 mM TCEP, 30 mM U-2H DHPC, 10 mM U-2H DMPC, 90% H2O/10% D2O.

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	DHPC	[U-2H]		30 mM
3	DMPC	[U-2H]		10 mM
4	TCEP	natural abundance		5 mM
5	phosphate buffer pH 5.8	natural abundance		50 mM
6	sodium azide	natural abundance		0.01 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.8, Details 0.01 % sodium azide, 50 mM phosphate buffer pH 5.8, 5 mM TCEP, 30 mM U-2H DHPC, 10 mM U-2H DMPC, 90% H2O/10% D2O.

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	DHPC	[U-2H]		30 mM
3	DMPC	[U-2H]		10 mM
4	TCEP	natural abundance		5 mM
5	phosphate buffer pH 5.8	natural abundance		50 mM
6	sodium azide	natural abundance		0.01 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.8, Details 0.01 % sodium azide, 50 mM phosphate buffer pH 5.8, 5 mM TCEP, 30 mM U-2H DHPC, 10 mM U-2H DMPC, 90% H2O/10% D2O.

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	DHPC	[U-2H]		30 mM
3	DMPC	[U-2H]		10 mM
4	TCEP	natural abundance		5 mM
5	phosphate buffer pH 5.8	natural abundance		50 mM
6	sodium azide	natural abundance		0.01 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.8, Details 0.01 % sodium azide, 50 mM phosphate buffer pH 5.8, 5 mM TCEP, 30 mM U-2H DHPC, 10 mM U-2H DMPC, 90% H2O/10% D2O.

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	DHPC	[U-2H]		30 mM
3	DMPC	[U-2H]		10 mM
4	TCEP	natural abundance		5 mM
5	phosphate buffer pH 5.8	natural abundance		50 mM
6	sodium azide	natural abundance		0.01 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34040_5lv6.nef
Input source #2: Coordindates	5lv6.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

----640-------650-------660-------670-------
EGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKR
||||||||||||||||||||||||||||||||||||||||||||
EGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKR
--------10--------20--------30--------40----

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

----640-------650-------660-------670-------
EGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKR
||||||||||||||||||||||||||||||||||||||||||||
EGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKR
--------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	44	0	0	100.0

Content subtype: combined_34040_5lv6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	484		100.0 (chain: A, length: 44)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	334 (1)	noe	68.2 (chain: A, length: 44), 68.2 (chain: B, length: 44)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	196 (1)	noe	61.4 (chain: A, length: 44), 61.4 (chain: B, length: 44)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	42 (1)	hbond	56.8 (chain: A, length: 44), 56.8 (chain: B, length: 44)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 252
  - ¹³C chemical shifts: 190
  - ¹⁵N chemical shifts: 42
- 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: 44, Sequence coverage: 68.2%
  - Entity_assembly_ID: B, Chain length: 44, Sequence coverage: 68.2%
- Total number of restraints: 334
- Weight of restraints: 1.0 (334)
- Potential type of restraints: upper-bound-parabolic (334)
- Range of distance target values: 2.7, 4.57 (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: DYANA/DIANA_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 61.4%
    - Entity_assembly_ID: B, Chain length: 44, Sequence coverage: 61.4%
  - Total number of restraints: 196
  - Weight of restraints: 1.0 (196)
  - Potential type of restraints: upper-bound-parabolic (196)
  - Range of distance target values: 2.55, 5.5 (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: DYANA/DIANA_distance_constraints_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 56.8%
      - Entity_assembly_ID: B, Chain length: 44, Sequence coverage: 56.8%
    - Total number of restraints: 42
    - Weight of restraints: 1.0 (42)
    - Potential type of restraints: upper-bound-parabolic (42)
    - Range of distance target values: 3.3, 3.3 (Å)
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
    - Distance restraints on contact map

Keywords Epidermal growth factor receptor, activation mechanism, bicelles, transferase