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Found 1 Document (1.378 seconds)

BMRB: 19562

2MFQ

NMR solution structures of FRS2a PTB domain with neurotrophin receptor TrkB

Authors

Zeng, L., Zhou, M.

Assembly

FRS2a PTB domain with neurotrophin receptor TrkB

Entity

1. FRS2a PTB domain with neurotrophin receptor TrkB, entity 1 (polymer), 115 monomers, 13423.90 Da Detail

SHMDTVPDNH RNKFKVINVD DDGNELGSGI MELTDTELIL YTRKRDSVKW HYLCLRRYGY DSNLFSFESG RRCQTGQGIF AFKCARAEEL FNMLQEIMQN NSINVVEEPV VERNN

2. FRS2a PTB domain with neurotrophin receptor TrkB, entity 2 (polymer, Thiol state: not present), 24 monomers, 2609.925 Da Detail

GGPDAVIIGM TKIPVIENPQ XFGI

Total weight

16033.825 Da

Max. entity weight

13423.9 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.8 %, Completeness: 81.4 %, Completeness (bb): 81.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.4 % (1319 of 1621)	85.6 % (725 of 847)	73.2 % (456 of 623)	91.4 % (138 of 151)
Backbone	81.7 % (668 of 818)	93.6 % (264 of 282)	69.2 % (279 of 403)	94.0 % (125 of 133)
Sidechain	81.8 % (761 of 930)	80.5 % (455 of 565)	84.7 % (294 of 347)	66.7 % (12 of 18)
Aromatic	54.8 % (69 of 126)	58.7 % (37 of 63)	50.0 % (31 of 62)	100.0 % (1 of 1)
Methyl	95.7 % (134 of 140)	95.7 % (67 of 70)	95.7 % (67 of 70)

1. entity 1

SHMDTVPDNH RNKFKVINVD DDGNELGSGI MELTDTELIL YTRKRDSVKW HYLCLRRYGY DSNLFSFESG RRCQTGQGIF AFKCARAEEL FNMLQEIMQN NSINVVEEPV VERNN

2. entity 2

GGPDAVIIGM TKIPVIENPQ XFGI

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	FRS2a PTB domain		0.0 ~ 0.0 mM
2	neurotrophin receptor TrkB		0.0 ~ 0.0 mM
3	sodium phosphate	natural abundance	100 mM
4	DTT	[U-100% 2H]	5 mM
5	EDTA	[U-100% 2H]	0.5 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	FRS2a PTB domain		0.0 ~ 0.0 mM
7	neurotrophin receptor TrkB		0.0 ~ 0.0 mM
8	sodium phosphate	natural abundance	100 mM
9	DTT	[U-100% 2H]	5 mM
10	EDTA	[U-100% 2H]	0.5 mM

Protein Blocks Logo

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

Release date

2014-02-11

Citation

Structural insights into FRS2α PTB domain recognition by neurotrophin receptor TrkB
Zeng, L., Kuti, M., Mujtaba, S., Zhou, M.
Proteins (2014), 82, 1534-1541, PubMed 24470253 , DOI 10.1002/prot.24523 , Abstract

Related entities 1. FRS2a PTB domain with neurotrophin receptor TrkB, entity 1, : 2 : 13 entities Detail

Related entities 2. FRS2a PTB domain with neurotrophin receptor TrkB, entity 2, : 1 : 8 : 15 entities Detail

Interaction partners 1. FRS2a PTB domain with neurotrophin receptor TrkB, entity 1, : 6 interactors Detail

More details for 6 interactors identified by 6 citations

Interaction partners 2. FRS2a PTB domain with neurotrophin receptor TrkB, entity 2, : 14 interactors Detail

More details for 14 interactors identified by 8 citations

Experiments performed 7 experiments Detail

1 3D HNCACB

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	FRS2a PTB domain		0.0 ~ 0.0 mM
7	neurotrophin receptor TrkB		0.0 ~ 0.0 mM
8	sodium phosphate	natural abundance	100 mM
9	DTT	[U-100% 2H]	5 mM
10	EDTA	[U-100% 2H]	0.5 mM

2 3D HNz(CO)CACB

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	FRS2a PTB domain		0.0 ~ 0.0 mM
7	neurotrophin receptor TrkB		0.0 ~ 0.0 mM
8	sodium phosphate	natural abundance	100 mM
9	DTT	[U-100% 2H]	5 mM
10	EDTA	[U-100% 2H]	0.5 mM

3 3D 1H-15N NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	FRS2a PTB domain		0.0 ~ 0.0 mM
7	neurotrophin receptor TrkB		0.0 ~ 0.0 mM
8	sodium phosphate	natural abundance	100 mM
9	DTT	[U-100% 2H]	5 mM
10	EDTA	[U-100% 2H]	0.5 mM

4 3D 1H-15N TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	FRS2a PTB domain		0.0 ~ 0.0 mM
7	neurotrophin receptor TrkB		0.0 ~ 0.0 mM
8	sodium phosphate	natural abundance	100 mM
9	DTT	[U-100% 2H]	5 mM
10	EDTA	[U-100% 2H]	0.5 mM

5 3D 1H-13C NOESY aliphatic

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	FRS2a PTB domain		0.0 ~ 0.0 mM
2	neurotrophin receptor TrkB		0.0 ~ 0.0 mM
3	sodium phosphate	natural abundance	100 mM
4	DTT	[U-100% 2H]	5 mM
5	EDTA	[U-100% 2H]	0.5 mM

6 3D 1H-13C NOESY aromatic

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	FRS2a PTB domain		0.0 ~ 0.0 mM
2	neurotrophin receptor TrkB		0.0 ~ 0.0 mM
3	sodium phosphate	natural abundance	100 mM
4	DTT	[U-100% 2H]	5 mM
5	EDTA	[U-100% 2H]	0.5 mM

7 3D 13C-edited 13C/15N-filtered NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	FRS2a PTB domain		0.0 ~ 0.0 mM
2	neurotrophin receptor TrkB		0.0 ~ 0.0 mM
3	sodium phosphate	natural abundance	100 mM
4	DTT	[U-100% 2H]	5 mM
5	EDTA	[U-100% 2H]	0.5 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19562_2mfq.nef
Input source #2: Coordindates	2mfq.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:19:GLN:C	2:20:PTR:N	unknown	unknown	n/a
2:20:PTR:C	2:21:PHE:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	512	PTR	O-PHOSPHOTYROSINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

--10-------20--------30--------40--------50--------60--------70--------80--------90-------100-------
SHMDTVPDNHRNKFKVINVDDDGNELGSGIMELTDTELILYTRKRDSVKWHYLCLRRYGYDSNLFSFESGRRCQTGQGIFAFKCARAEELFNMLQEIMQN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SHMDTVPDNHRNKFKVINVDDDGNELGSGIMELTDTELILYTRKRDSVKWHYLCLRRYGYDSNLFSFESGRRCQTGQGIFAFKCARAEELFNMLQEIMQN
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

110-------120--
NSINVVEEPVVERNN
|||||||||||||||
NSINVVEEPVVERNN
-------110-----

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

-----500-------510-----
GPDAVIIGMTKIPVIENPQXFGI
|||||||||||||||||||||||
GPDAVIIGMTKIPVIENPQXFGI
--------10--------20---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	115	0	0	100.0
B	B	23	0	0	100.0

Content subtype: combined_19562_2mfq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1276		100.0 (chain: A, length: 115), 95.7 (chain: B, length: 23)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	97 (1)	hbond	51.3 (chain: A, length: 115)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	152 (152)	.	75.7 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 23, Sequence coverage: 95.7%
- Total number of assignments
  - ¹H chemical shifts: 721
  - ¹³C chemical shifts: 421
  - ¹⁵N chemical shifts: 134
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	712	609	85.5
¹³C chemical shifts	520	349	67.1
¹⁵N chemical shifts	138	120	87.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	235	227	96.6
¹³C chemical shifts	230	106	46.1
¹⁵N chemical shifts	113	108	95.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	477	382	80.1
¹³C chemical shifts	290	243	83.8
¹⁵N chemical shifts	25	12	48.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	56	96.6
¹³C chemical shifts	58	56	96.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	35	60.3
¹³C chemical shifts	57	30	52.6
¹⁵N chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	140	111	79.3
¹³C chemical shifts	108	70	64.8
¹⁵N chemical shifts	22	14	63.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	37	80.4
¹³C chemical shifts	46	21	45.7
¹⁵N chemical shifts	20	13	65.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	74	78.7
¹³C chemical shifts	62	49	79.0
¹⁵N chemical shifts	2	1	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	15	88.2
¹³C chemical shifts	17	15	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	4	44.4
¹³C chemical shifts	9	2	22.2

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: hbond
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 51.3%
- Total number of restraints: 97
- Weight of restraints: 1.0 (97)
- Potential type of restraints: square-well-parabolic (97)
- Range of distance target values: 1.8, 3.1 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 75.7%
- Total number of restraints: 152
- Total number of restraints per polymer type: 152
- Weight of restraints: 1.0 (152)
- Potential type of restraints: square-well-parabolic (152)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords FGFR, FRS2, PTB, SNT, Trk

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Found 1 Document (1.378 seconds)

BMRB: 19562

Sample #1

Sample #2

Related entities 1. FRS2a PTB domain with neurotrophin receptor TrkB, entity 1, : 2 : 13 entities Detail

Related entities 2. FRS2a PTB domain with neurotrophin receptor TrkB, entity 2, : 1 : 8 : 15 entities Detail

Interaction partners 1. FRS2a PTB domain with neurotrophin receptor TrkB, entity 1, : 6 interactors Detail

Interaction partners 2. FRS2a PTB domain with neurotrophin receptor TrkB, entity 2, : 14 interactors Detail

Experiments performed 7 experiments Detail

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NMR combined restraints 4 contents Detail