BMRBj - BMREntryMaster

Found 1 Document (1.7 seconds)

BMRB: 34154

5OB4

NMR spatial structure of HER2 TM domain dimer in DPC micelles

Authors

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

Assembly

Receptor tyrosine-protein kinase erbB-2 (E.C.2.7.10.1)

Entity

1. Receptor tyrosine-protein kinase erbB-2 (E.C.2.7.10.1) (polymer), 44 monomers, 4727.746 × 2 Da Detail

GCPAEQRASP LTSIISAVVG ILLVVVLGVV FGILIKRRQQ KIRK

Total weight

9455.492 Da

Max. entity weight

4727.746 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: 96.0 %, Completeness (bb): 98.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.0 % (502 of 523)	95.2 % (259 of 272)	98.1 % (202 of 206)	91.1 % (41 of 45)
Backbone	98.8 % (257 of 260)	98.9 % (89 of 90)	99.2 % (127 of 128)	97.6 % (41 of 42)
Sidechain	93.7 % (284 of 303)	93.4 % (170 of 182)	96.6 % (114 of 118)	0.0 % (0 of 3)
Aromatic	80.0 % (8 of 10)	100.0 % (5 of 5)	60.0 % (3 of 5)
Methyl	100.0 % (80 of 80)	100.0 % (40 of 40)	100.0 % (40 of 40)

1. entity 1

GCPAEQRASP LTSIISAVVG ILLVVVLGVV FGILIKRRQQ KIRK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 313 K, pH 6.0 (±0.1), Details 2.5 mM [U-100% 13C; U-100% 15N] HER2TM, 2.5 mM HER2TM, 200 mM [U-99% 2H] DPC, 20 mM potassium phosphate, 0.01 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DPC	[U-99% 2H]	200 mM
2	HER2TM	natural abundance	2.5 mM
3	HER2TM_label	[U-100% 13C; U-100% 15N]	2.5 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.01 %

Protein Blocks Logo

Calculated from 10 models in PDB: 5OB4, Strand ID: A, B Detail

Release date

2017-11-12

Citation

NMR relaxation parameters of methyl groups as a tool to map the interfaces of helix-helix interactions in membrane proteins
Lesovoy, D.M., Mineev, K.S., Bragin, P.E., Bocharova, O.V., Bocharov, E.V., Arseniev, A.S.
J. Biomol. NMR (2017), 69, 165-179, PubMed 29063258 , DOI 10.1007/s10858-017-0146-1 , Abstract

Related entities 1. Receptor tyrosine-protein kinase erbB-2 (E.C.2.7.10.1), : 1 : 4 : 1 : 49 entities Detail

Interaction partners 1. Receptor tyrosine-protein kinase erbB-2 (E.C.2.7.10.1), : 119 interactors Detail

More details for 119 interactors identified by 37 citations

Experiments performed 6 experiments Detail

1 3D HNCA

Instrument

Bruker av600 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 313 K, pH 6.0 (±0.1), Details 2.5 mM [U-100% 13C; U-100% 15N] HER2TM, 2.5 mM HER2TM, 200 mM [U-99% 2H] DPC, 20 mM potassium phosphate, 0.01 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DPC	[U-99% 2H]	200 mM
2	HER2TM	natural abundance	2.5 mM
3	HER2TM_label	[U-100% 13C; U-100% 15N]	2.5 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.01 %

2 3D HNCO

Instrument

Bruker av600 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DPC	[U-99% 2H]	200 mM
2	HER2TM	natural abundance	2.5 mM
3	HER2TM_label	[U-100% 13C; U-100% 15N]	2.5 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.01 %

3 3D HCCH-TOCSY

Instrument

Bruker av600 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DPC	[U-99% 2H]	200 mM
2	HER2TM	natural abundance	2.5 mM
3	HER2TM_label	[U-100% 13C; U-100% 15N]	2.5 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.01 %

4 3D 1H-13C NOESY aliphatic

Instrument

Bruker av600 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DPC	[U-99% 2H]	200 mM
2	HER2TM	natural abundance	2.5 mM
3	HER2TM_label	[U-100% 13C; U-100% 15N]	2.5 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.01 %

5 3D 1H-15N NOESY

Instrument

Bruker av600 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DPC	[U-99% 2H]	200 mM
2	HER2TM	natural abundance	2.5 mM
3	HER2TM_label	[U-100% 13C; U-100% 15N]	2.5 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.01 %

6 3D 13C-filtered NOESY

Instrument

Bruker av600 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DPC	[U-99% 2H]	200 mM
2	HER2TM	natural abundance	2.5 mM
3	HER2TM_label	[U-100% 13C; U-100% 15N]	2.5 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.01 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34154_5ob4.nef
Input source #2: Coordindates	5ob4.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

--------10--------20--------30--------40----
GCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRK
||||||||||||||||||||||||||||||||||||||||||||
GCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRK

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

-------110-------120-------130-------140----
GCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRK
||||||||||||||||||||||||||||||||||||||||||||
GCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRK
--------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_34154_5ob4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	508		100.0 (chain: A, length: 44)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	826 (1)	noe	100.0 (chain: A, length: 44), 100.0 (chain: B, length: 44)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	1546 (1546)	.	97.7 (chain: A, length: 44), 97.7 (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: 259
  - ¹³C chemical shifts: 202
  - ¹⁵N chemical shifts: 47
- 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)
3	PRO	N	138.718
10	PRO	N	137.92

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	272	259	95.2
¹³C chemical shifts	206	202	98.1
¹⁵N chemical shifts	49	45	91.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	90	89	98.9
¹³C chemical shifts	88	88	100.0
¹⁵N chemical shifts	42	41	97.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	182	170	93.4
¹³C chemical shifts	118	114	96.6
¹⁵N chemical shifts	7	4	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	40	100.0
¹³C chemical shifts	40	40	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0
¹³C chemical shifts	5	3	60.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 44, Sequence coverage: 100.0%
- Total number of restraints: 826
- Weight of restraints: 1.0 (826)
- Potential type of restraints: upper-bound-parabolic (826)
- Range of distance target values: 0.0, 5.31 (Å)
- Histogram of 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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 97.7%
  - Entity_assembly_ID: B, Chain length: 44, Sequence coverage: 97.7%
- Total number of restraints: 1546
- Total number of restraints per polymer type: 1546
- Weight of restraints: 1.0 (1546)
- Potential type of restraints: square-well-parabolic (1546)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords MEMBRANE PROTEIN, PROTEIN ERBB2 HER2 RECEPTOR TYROSINE KINASE MEMBRANE DOMAIN DIMER

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 (1.7 seconds)

BMRB: 34154

Sample

Related entities 1. Receptor tyrosine-protein kinase erbB-2 (E.C.2.7.10.1), : 1 : 4 : 1 : 49 entities Detail

Interaction partners 1. Receptor tyrosine-protein kinase erbB-2 (E.C.2.7.10.1), : 119 interactors Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail