BMRBj - BMREntryMaster

Found 1 Document (0.59 seconds)

BMRB: 25593

2N2A

Spatial structure of HER2/ErbB2 dimeric transmembrane domain in the presence of cytoplasmic juxtamembrane domains

Authors

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

Assembly

HER2/ErbB2 dimeric transmembrane domain

Entity

1. HER2/ErbB2 dimeric transmembrane domain (polymer, Thiol state: not present), 58 monomers, 6500.784 × 2 Da Detail

AEQRASPLTS IISAVVGILL VVVLGVVFGI LIKRRQQKIR KYTMRRLLQE TELVEPLG

Total weight

13001.568 Da

Max. entity weight

6500.784 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.6 %, Completeness: 84.1 %, Completeness (bb): 87.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.1 % (594 of 706)	86.7 % (319 of 368)	79.5 % (221 of 278)	90.0 % (54 of 60)
Backbone	87.5 % (301 of 344)	96.6 % (114 of 118)	78.8 % (134 of 170)	94.6 % (53 of 56)
Sidechain	79.8 % (332 of 416)	80.0 % (200 of 250)	81.5 % (132 of 162)	0.0 % (0 of 4)
Aromatic	22.2 % (4 of 18)	44.4 % (4 of 9)	0.0 % (0 of 9)
Methyl	94.2 % (98 of 104)	94.2 % (49 of 52)	94.2 % (49 of 52)

1. entity

AEQRASPLTS IISAVVGILL VVVLGVVFGI LIKRRQQKIR KYTMRRLLQE TELVEPLG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5

#	Name	Isotope labeling	Concentration
1	DPC	[U-100% 2H]	4 mg
2	labeled protein	[U-100% 13C; U-100% 15N]	1 mg
3	unlabeled protein	natural abundance	1 mg
4	sodium acetate	natural abundance	50 mM
5	sodium azide	natural abundance	1e-3 %
6	D2O	[U-99% 2H]	100 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5

#	Name	Isotope labeling	Concentration
7	DPC	[U-100% 2H]	4 mg
8	labeled protein	[U-100% 13C; U-100% 15N]	1 mg
9	sodium acetate	natural abundance	50 mM
10	sodium azide	natural abundance	1e-3 %
11	D2O	[U-99% 2H]	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5

#	Name	Isotope labeling	Concentration
12	DPC	[U-100% 2H]	4 mg
13	labeled protein	[U-100% 13C; U-100% 15N]	1 mg
14	sodium acetate	natural abundance	50 mM
15	sodium azide	natural abundance	1e-3 %
16	H2O	natural abundance	90 %
17	D2O	[U-99% 2H]	10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2N2A, Strand ID: A, B Detail

Release date

2016-02-21

Citation

HER2 Transmembrane Domain Dimerization Coupled with Self-Association of Membrane-Embedded Cytoplasmic Juxtamembrane Regions
Bragin, P., Mineev, K., Bocharova, O., Bocharov, E., Arseniev, A.
J. Mol. Biol. (2016), 428, 52-61, PubMed 26585403 , DOI 10.1016/j.jmb.2015.11.007 , Abstract

Related entities 1. HER2/ErbB2 dimeric transmembrane domain, : 1 : 2 : 43 entities Detail

Experiments performed 8 experiments Detail

1 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5

#	Name	Isotope labeling	Concentration
7	DPC	[U-100% 2H]	4 mg
8	labeled protein	[U-100% 13C; U-100% 15N]	1 mg
9	sodium acetate	natural abundance	50 mM
10	sodium azide	natural abundance	1e-3 %
11	D2O	[U-99% 2H]	100 %

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5

#	Name	Isotope labeling	Concentration
12	DPC	[U-100% 2H]	4 mg
13	labeled protein	[U-100% 13C; U-100% 15N]	1 mg
14	sodium acetate	natural abundance	50 mM
15	sodium azide	natural abundance	1e-3 %
16	H2O	natural abundance	90 %
17	D2O	[U-99% 2H]	10 %

3 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5

#	Name	Isotope labeling	Concentration
7	DPC	[U-100% 2H]	4 mg
8	labeled protein	[U-100% 13C; U-100% 15N]	1 mg
9	sodium acetate	natural abundance	50 mM
10	sodium azide	natural abundance	1e-3 %
11	D2O	[U-99% 2H]	100 %

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5

#	Name	Isotope labeling	Concentration
12	DPC	[U-100% 2H]	4 mg
13	labeled protein	[U-100% 13C; U-100% 15N]	1 mg
14	sodium acetate	natural abundance	50 mM
15	sodium azide	natural abundance	1e-3 %
16	H2O	natural abundance	90 %
17	D2O	[U-99% 2H]	10 %

5 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5

#	Name	Isotope labeling	Concentration
12	DPC	[U-100% 2H]	4 mg
13	labeled protein	[U-100% 13C; U-100% 15N]	1 mg
14	sodium acetate	natural abundance	50 mM
15	sodium azide	natural abundance	1e-3 %
16	H2O	natural abundance	90 %
17	D2O	[U-99% 2H]	10 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5

#	Name	Isotope labeling	Concentration
12	DPC	[U-100% 2H]	4 mg
13	labeled protein	[U-100% 13C; U-100% 15N]	1 mg
14	sodium acetate	natural abundance	50 mM
15	sodium azide	natural abundance	1e-3 %
16	H2O	natural abundance	90 %
17	D2O	[U-99% 2H]	10 %

7 3D HCACO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5

#	Name	Isotope labeling	Concentration
12	DPC	[U-100% 2H]	4 mg
13	labeled protein	[U-100% 13C; U-100% 15N]	1 mg
14	sodium acetate	natural abundance	50 mM
15	sodium azide	natural abundance	1e-3 %
16	H2O	natural abundance	90 %
17	D2O	[U-99% 2H]	10 %

8 3D 1H-15N TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5

#	Name	Isotope labeling	Concentration
7	DPC	[U-100% 2H]	4 mg
8	labeled protein	[U-100% 13C; U-100% 15N]	1 mg
9	sodium acetate	natural abundance	50 mM
10	sodium azide	natural abundance	1e-3 %
11	D2O	[U-99% 2H]	100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25593_2n2a.nef
Input source #2: Coordindates	2n2a.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--------50--------
AEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLG

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

-------110-------120-------130-------140-------150--------
AEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLG
--------10--------20--------30--------40--------50--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	58	0	0	100.0
B	B	58	0	0	100.0

Content subtype: combined_25593_2n2a.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	591		96.6 (chain: A, length: 58)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1236 (1)	noe	96.6 (chain: A, length: 58), 96.6 (chain: B, length: 58)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	31 (1)	noe	24.1 (chain: A, length: 58), 25.9 (chain: B, length: 58)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	52 (1)	hbond	51.7 (chain: A, length: 58), 51.7 (chain: B, length: 58)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 96.6%
- Total number of assignments
  - ¹H chemical shifts: 318
  - ¹³C chemical shifts: 219
  - ¹⁵N chemical shifts: 54
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	368	317	86.1
¹³C chemical shifts	278	219	78.8
¹⁵N chemical shifts	66	54	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	118	113	95.8
¹³C chemical shifts	116	83	71.6
¹⁵N chemical shifts	56	54	96.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	250	204	81.6
¹³C chemical shifts	162	136	84.0
¹⁵N chemical shifts	10	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	51	96.2
¹³C chemical shifts	53	51	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	4	44.4
¹³C chemical shifts	9	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 96.6%
  - Entity_assembly_ID: B, Chain length: 58, Sequence coverage: 96.6%
- Total number of restraints: 1235
- Weight of restraints: 1.0 (1235)
- Potential type of restraints: upper-bound-parabolic (1235)
- Range of distance target values: 2.4, 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_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 24.1%
    - Entity_assembly_ID: B, Chain length: 58, Sequence coverage: 25.9%
  - Total number of restraints: 31
  - Weight of restraints: 1.0 (31)
  - Potential type of restraints: upper-bound-parabolic (31)
  - Range of distance target values: 3.0, 5.29 (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: 58, Sequence coverage: 51.7%
      - Entity_assembly_ID: B, Chain length: 58, Sequence coverage: 51.7%
    - Total number of restraints: 52
    - Weight of restraints: 1.0 (52)
    - Potential type of restraints: upper-bound-parabolic (52)
    - Range of distance target values: 3.2, 3.3 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
    - Distance restraints on contact map

Keywords Activation, ErbB2, HER2, Tyrosine kinase, transmembrane

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 (0.59 seconds)

BMRB: 25593

Sample #1

Sample #2

Sample #3

Related entities 1. HER2/ErbB2 dimeric transmembrane domain, : 1 : 2 : 43 entities Detail

Experiments performed 8 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail