BMRBj - BMREntryMaster

Found 1 Document (0.671 seconds)

BMRB: 50265

NMR backbone resonance assignment of TREM2 transmembrane helix in complex with the partner protein DAP12

Authors

Steiner, A., Hagn, F.X.

Assembly

TREM2 TMH wt + DAP12

Entity

1. TREM2 TMH wt + DAP12, entity 1 (polymer, Thiol state: all free), 49 monomers, 5167.076 Da Detail

GSGRSLLEGE IPFPPTSILL LLACIFLIKI LAASALWAAA WHGQKPGTH

2. TREM2 TMH wt + DAP12, entity 2 (polymer, Thiol state: not present), 50 monomers, 5140.030 Da Detail

GLRPVQAQAQ SDSSCSTVSP GVLAGIVMGD LVLTVLIALA VYFLGRLVPR

Total weight

10307.105 Da

Max. entity weight

5167.076 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 41.4 %, Completeness: 15.7 %, Completeness (bb): 28.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	15.7 % (174 of 1111)	7.4 % (42 of 565)	21.7 % (97 of 448)	35.7 % (35 of 98)
Backbone	28.8 % (167 of 580)	18.4 % (37 of 201)	33.1 % (95 of 287)	38.0 % (35 of 92)
Sidechain	5.6 % (35 of 620)	1.6 % (6 of 364)	11.6 % (29 of 250)	0.0 % (0 of 6)
Aromatic	0.0 % (0 of 70)	0.0 % (0 of 35)	0.0 % (0 of 33)	0.0 % (0 of 2)
Methyl	5.0 % (8 of 160)	1.3 % (1 of 80)	8.7 % (7 of 80)

1. entity 1

GSGRSLLEGE IPFPPTSILL LLACIFLIKI LAASALWAAA WHGQKPGTH

2. entity 2

GLRPVQAQAQ SDSSCSTVSP GVLAGIVMGD LVLTVLIALA VYFLGRLVPR

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7, Details 500 uM TREM2-TMH wt + unlabelled DAP12 in 300mM DPC 20 mM NaPi pH7.0 50 mM NaCl 0.5 mM EDTA 5 mM DTT

#	Name	Isotope labeling	Concentration
1	TREM2 TMH wt	[U-13C; U-15N; U-2H]	500 (±50.0) uM
2	DAP12	natural abundance	1000 (±50.0) uM
3	DPC	natural abundance	300 mM
4	NaPi	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.5 mM
7	DTT	natural abundance	5 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6Z0I, Strand ID: A Detail

Release date

2020-05-07

Citation

γ-Secretase cleavage of the Alzheimer risk factor TREM2 is determined by its intrinsic structural dynamics
Steiner, A., Schlepckow, K., Brunner, B., Steiner, H., Haass, C., Hagn, F.X.
EMBO J. (2020), 39, e104247-e104247, PubMed 32830336 , DOI 10.15252/embj.2019104247 , Abstract

Related entities 1. TREM2 TMH wt + DAP12, entity 1, : 2 : 2 entities Detail

Related entities 2. TREM2 TMH wt + DAP12, entity 2, : 3 : 25 entities Detail

Interaction partners 1. TREM2 TMH wt + DAP12, entity 1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Interaction partners 2. TREM2 TMH wt + DAP12, entity 2, : 11 : 1 interactors Detail

More details for 12 interactors identified by 7 citations

Experiments performed 6 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7, Details 500 uM TREM2-TMH wt + unlabelled DAP12 in 300mM DPC 20 mM NaPi pH7.0 50 mM NaCl 0.5 mM EDTA 5 mM DTT

#	Name	Isotope labeling	Concentration
1	TREM2 TMH wt	[U-13C; U-15N; U-2H]	500 (±50.0) uM
2	DAP12	natural abundance	1000 (±50.0) uM
3	DPC	natural abundance	300 mM
4	NaPi	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.5 mM
7	DTT	natural abundance	5 mM

2 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TREM2 TMH wt	[U-13C; U-15N; U-2H]	500 (±50.0) uM
2	DAP12	natural abundance	1000 (±50.0) uM
3	DPC	natural abundance	300 mM
4	NaPi	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.5 mM
7	DTT	natural abundance	5 mM

3 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TREM2 TMH wt	[U-13C; U-15N; U-2H]	500 (±50.0) uM
2	DAP12	natural abundance	1000 (±50.0) uM
3	DPC	natural abundance	300 mM
4	NaPi	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.5 mM
7	DTT	natural abundance	5 mM

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TREM2 TMH wt	[U-13C; U-15N; U-2H]	500 (±50.0) uM
2	DAP12	natural abundance	1000 (±50.0) uM
3	DPC	natural abundance	300 mM
4	NaPi	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.5 mM
7	DTT	natural abundance	5 mM

5 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TREM2 TMH wt	[U-13C; U-15N; U-2H]	500 (±50.0) uM
2	DAP12	natural abundance	1000 (±50.0) uM
3	DPC	natural abundance	300 mM
4	NaPi	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.5 mM
7	DTT	natural abundance	5 mM

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TREM2 TMH wt	[U-13C; U-15N; U-2H]	500 (±50.0) uM
2	DAP12	natural abundance	1000 (±50.0) uM
3	DPC	natural abundance	300 mM
4	NaPi	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.5 mM
7	DTT	natural abundance	5 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr50265_3.str
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	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr50265_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	159		77.6 (chain: 1, length: 49)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 49, Sequence coverage: 77.6%
- Total number of assignments
  - ¹³C chemical shifts: 91
  - ¹H chemical shifts: 34
  - ¹⁵N chemical shifts: 34
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	229	91	39.7
¹H chemical shifts	289	34	11.8
¹⁵N chemical shifts	49	34	69.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	98	66	67.3
¹H chemical shifts	99	34	34.3
¹⁵N chemical shifts	45	34	75.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	131	25	19.1
¹H chemical shifts	190	0	0.0
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	37	4	10.8
¹H chemical shifts	37	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	24	0	0.0
¹H chemical shifts	26	0	0.0
¹⁵N chemical shifts	2	0	0.0

Keywords NMR, TREM2, dynamics, intramembrane protease, structure

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 (0.671 seconds)

BMRB: 50265

Sample

Related entities 1. TREM2 TMH wt + DAP12, entity 1, : 2 : 2 entities Detail

Related entities 2. TREM2 TMH wt + DAP12, entity 2, : 3 : 25 entities Detail

Interaction partners 1. TREM2 TMH wt + DAP12, entity 1, : 1 interactors Detail

Interaction partners 2. TREM2 TMH wt + DAP12, entity 2, : 11 : 1 interactors Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 4 contents Detail