BMRBj - BMREntryMaster

Found 1 Document (0.84 seconds)

BMRB: 17488

2L9U

Spatial structure of dimeric ErbB3 transmembrane domain

Authors

Mineev, K.S., Arseniev, A.S.

Assembly

ErbB3tm

Entity

1. ErbB3tm (polymer, Thiol state: not present), 40 monomers, 4692.569 × 2 Da Detail

MGRTHLTMAL TVIAGLVVIF MMLGGTFLYW RGRRHHHHHH

Total weight

9385.138 Da

Max. entity weight

4692.569 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.5 %, Completeness (bb): 98.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.5 % (448 of 479)	95.1 % (231 of 243)	90.3 % (176 of 195)	100.0 % (41 of 41)
Backbone	98.8 % (237 of 240)	98.8 % (84 of 85)	98.3 % (113 of 115)	100.0 % (40 of 40)
Sidechain	89.4 % (245 of 274)	93.0 % (147 of 158)	84.3 % (97 of 115)	100.0 % (1 of 1)
Aromatic	63.2 % (43 of 68)	76.5 % (26 of 34)	48.5 % (16 of 33)	100.0 % (1 of 1)
Methyl	100.0 % (52 of 52)	100.0 % (26 of 26)	100.0 % (26 of 26)

1. ErbB3tm

MGRTHLTMAL TVIAGLVVIF MMLGGTFLYW RGRRHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
2	ErbB3tm	natural abundance	1 mM
3	DPC	[U-99% 2H]	80 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
7	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
8	ErbB3tm	natural abundance	1 mM
9	DPC	[U-99% 2H]	80 mM
10	sodium azide	natural abundance	1 mM
11	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2L9U, Strand ID: A, B Detail

Release date

2011-05-09

Citation

Spatial structure and dimer--monomer equilibrium of the ErbB3 transmembrane domain in DPC micelles
Mineev, K.S., Khabibullina, N.F., Lyukmanova, E.N., Dolgikh, D.A., Kirpichnikov, M.P., Arseniev, A.S.
Biochim. Biophys. Acta (2011), 1808, 2081-2088, PubMed 21575594 , DOI 10.1016/j.bbamem.2011.04.017 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: P21860 released on 1991-05-01
Title ERBB3_HUMAN Entity Receptor tyrosine-protein kinase erbB-3

Related entities 1. ErbB3tm, : 1 : 10 entities Detail

Experiments performed 10 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
2	ErbB3tm	natural abundance	1 mM
3	DPC	[U-99% 2H]	80 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
2	ErbB3tm	natural abundance	1 mM
3	DPC	[U-99% 2H]	80 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
2	ErbB3tm	natural abundance	1 mM
3	DPC	[U-99% 2H]	80 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
2	ErbB3tm	natural abundance	1 mM
3	DPC	[U-99% 2H]	80 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

5 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
7	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
8	ErbB3tm	natural abundance	1 mM
9	DPC	[U-99% 2H]	80 mM
10	sodium azide	natural abundance	1 mM
11	D2O	natural abundance	100 %

6 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
2	ErbB3tm	natural abundance	1 mM
3	DPC	[U-99% 2H]	80 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

7 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
7	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
8	ErbB3tm	natural abundance	1 mM
9	DPC	[U-99% 2H]	80 mM
10	sodium azide	natural abundance	1 mM
11	D2O	natural abundance	100 %

8 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
7	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
8	ErbB3tm	natural abundance	1 mM
9	DPC	[U-99% 2H]	80 mM
10	sodium azide	natural abundance	1 mM
11	D2O	natural abundance	100 %

9 3D 15N,13C-filtered, 13C-edited NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
7	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
8	ErbB3tm	natural abundance	1 mM
9	DPC	[U-99% 2H]	80 mM
10	sodium azide	natural abundance	1 mM
11	D2O	natural abundance	100 %

10 3D 15N,13C-filtered, 13C-edited NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	ErbB3tm	[U-100% 13C; U-100% 15N]	1 mM
2	ErbB3tm	natural abundance	1 mM
3	DPC	[U-99% 2H]	80 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_17488_2l9u.nef
Input source #2: Coordindates	2l9u.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------
MGRTHLTMALTVIAGLVVIFMMLGGTFLYWRGRRHHHHHH
||||||||||||||||||||||||||||||||||||||||
MGRTHLTMALTVIAGLVVIFMMLGGTFLYWRGRRHHHHHH
--------10--------20--------30--------40

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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	40	0	0	100.0
B	B	40	0	0	100.0

Content subtype: combined_17488_2l9u.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	465		100.0 (chain: A, length: 40)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	978 (1)	noe	95.0 (chain: A, length: 40), 95.0 (chain: B, length: 40)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	107 (107)	.	80.0 (chain: A, length: 40)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 100.0%

---640-----650-------660-------670------
MGRTHLTMALTVIAGLVVIFMMLGGTFLYWRGRRHHHHHH
||||||||||||||||||||||||||||||||||||||||
MGRTHLTMALTVIAGLVVIFMMLGGTFLYWRGRRHHHHHH

Total number of assignments
- ¹H chemical shifts: 242
- ¹³C chemical shifts: 176
- ¹⁵N chemical shifts: 47

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
640	THR	HG1	4.647
643	THR	HG1	4.636
647	THR	HG1	4.646
662	THR	HG1	4.642
667	ARG	HH11	6.99
667	ARG	HH12	6.99
667	ARG	NH1	72.219
669	ARG	HH21	6.835
669	ARG	HH22	6.835
669	ARG	NH2	72.181
670	ARG	HH21	6.851
670	ARG	HH22	6.851
670	ARG	NH2	72.179

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	243	231	95.1
¹³C chemical shifts	195	176	90.3
¹⁵N chemical shifts	45	44	97.8

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	85	83	97.6
¹³C chemical shifts	80	79	98.8
¹⁵N chemical shifts	40	40	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	158	148	93.7
¹³C chemical shifts	115	97	84.3
¹⁵N chemical shifts	5	4	80.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	30	100.0
¹³C chemical shifts	30	30	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	26	76.5
¹³C chemical shifts	33	16	48.5
¹⁵N chemical shifts	1	1	100.0

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: 40, Sequence coverage: 95.0%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 95.0%
- Total number of restraints: 978
- Weight of restraints: 1.0 (978)
- Potential type of restraints: upper-bound-parabolic (978)
- Range of distance target values: 0.0, 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 80.0%
- Total number of restraints: 107
- Total number of restraints per polymer type: 107
- Weight of restraints: 1.0 (107)
- Potential type of restraints: square-well-parabolic (107)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords EGFR, ErbB, membrane protein, NMR, transmenbrane dimer

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Found 1 Document (0.84 seconds)

BMRB: 17488

Sample #1

Sample #2

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. ErbB3tm, : 1 : 10 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 4 contents Detail