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Found 1 Document (1.896 seconds)

BMRB: 17538

2LAW

Structure of the second WW domain from human YAP in complex with a human Smad1 derived peptide

Authors

Macias, M.J., Aragon, E., Goerner, N., Zaromytidou, A., Xi, Q., Escobedo, A., Massague, J.

Assembly

second WW domain from human YAP in complex with a human Smad1 derived peptide

Entity

1. second WW domain from human YAP (polymer, Thiol state: not present), 38 monomers, 4363.793 Da Detail

GAMEGPLPDG WEQAMTQDGE IYYINHKNKT TSWLDPRL

2. human Smad1 derived peptide (polymer, Thiol state: not present), 12 monomers, 1293.418 Da Detail

TPPPAYLPPE DP

Total weight

5657.211 Da

Max. entity weight

4363.793 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 68.0 %, Completeness: 50.0 %, Completeness (bb): 57.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	50.0 % (291 of 582)	63.8 % (196 of 307)	28.1 % (64 of 228)	66.0 % (31 of 47)
Backbone	57.1 % (161 of 282)	70.5 % (67 of 95)	43.8 % (64 of 146)	73.2 % (30 of 41)
Sidechain	46.2 % (160 of 346)	60.8 % (129 of 212)	23.4 % (30 of 128)	16.7 % (1 of 6)
Aromatic	32.7 % (17 of 52)	65.4 % (17 of 26)	0.0 % (0 of 24)	0.0 % (0 of 2)
Methyl	39.5 % (15 of 38)	73.7 % (14 of 19)	5.3 % (1 of 19)

1. second WW domain from human YAP

GAMEGPLPDG WEQAMTQDGE IYYINHKNKT TSWLDPRL

2. human Smad1 derived peptide

TPPPAYLPPE DP

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7, Details Unlabeled sample

#	Name	Isotope labeling	Concentration
1	NEDD4LWW3	natural abundance	1 mM
2	SMAD3	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	2 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7, Details 15N labeled sample

#	Name	Isotope labeling	Concentration
8	NEDD4LWW3	[U-100% 15N]	1 mM
9	SMAD3	natural abundance	3 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	100 mM
12	sodium azide	natural abundance	2 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7, Details 15N,13C labeled sample

#	Name	Isotope labeling	Concentration
15	NEDD4LWW3	[U-100% 13C; U-100% 15N]	1 mM
16	SMAD3	natural abundance	3 mM
17	sodium phosphate	natural abundance	20 mM
18	sodium chloride	natural abundance	100 mM
19	sodium azide	natural abundance	2 mM
20	H2O	natural abundance	90 %
21	D2O	natural abundance	10 %

Protein Blocks Logo

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

Release date

2011-06-22

Citation

A Smad action turnover switch operated by WW domain readers of a phosphoserine code
Aragon, E., Goerner, N., Zaromytidou, A., Xi, Q., Escobedo, A., Massague, J., Macias, M.J.
Genes. Dev. (2011), 25, 1275-1288, PubMed 21685363 , DOI 10.1101/gad.2060811 , Abstract

Related entities 1. second WW domain from human YAP, : 398 entities Detail

Related entities 2. human Smad1 derived peptide, : 1 : 4 : 1 : 1 entities Detail

Interaction partners 1. second WW domain from human YAP, : 61 interactors Detail

More details for 61 interactors identified by 31 citations

Experiments performed 5 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7, Details Unlabeled sample

#	Name	Isotope labeling	Concentration
1	NEDD4LWW3	natural abundance	1 mM
2	SMAD3	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	2 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 2D 1H-1H TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7, Details Unlabeled sample

#	Name	Isotope labeling	Concentration
1	NEDD4LWW3	natural abundance	1 mM
2	SMAD3	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	2 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7, Details 15N,13C labeled sample

#	Name	Isotope labeling	Concentration
15	NEDD4LWW3	[U-100% 13C; U-100% 15N]	1 mM
16	SMAD3	natural abundance	3 mM
17	sodium phosphate	natural abundance	20 mM
18	sodium chloride	natural abundance	100 mM
19	sodium azide	natural abundance	2 mM
20	H2O	natural abundance	90 %
21	D2O	natural abundance	10 %

4 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7, Details 15N,13C labeled sample

#	Name	Isotope labeling	Concentration
15	NEDD4LWW3	[U-100% 13C; U-100% 15N]	1 mM
16	SMAD3	natural abundance	3 mM
17	sodium phosphate	natural abundance	20 mM
18	sodium chloride	natural abundance	100 mM
19	sodium azide	natural abundance	2 mM
20	H2O	natural abundance	90 %
21	D2O	natural abundance	10 %

5 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7, Details 15N labeled sample

#	Name	Isotope labeling	Concentration
8	NEDD4LWW3	[U-100% 15N]	1 mM
9	SMAD3	natural abundance	3 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	100 mM
12	sodium azide	natural abundance	2 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17538_2law.nef
Input source #2: Coordindates	2law.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

--230-------240-------250-------260---
GAMEGPLPDGWEQAMTQDGEIYYINHKNKTTSWLDPRL
||||||||||||||||||||||||||||||||||||||
GAMEGPLPDGWEQAMTQDGEIYYINHKNKTTSWLDPRL
--------10--------20--------30--------

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

------230---
TPPPAYLPPEDP
||||||||||||
TPPPAYLPPEDP
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	38	0	0	100.0
B	B	12	0	0	100.0

Content subtype: combined_17538_2law.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	293		89.5 (chain: A, length: 38)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	310 (1)	noe	94.7 (chain: A, length: 38), 33.3 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 38, Sequence coverage: 89.5%
- Total number of assignments
  - ¹H chemical shifts: 199
  - ¹³C chemical shifts: 64
  - ¹⁵N chemical shifts: 30
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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)
241	THR	HG1	6.775
251	HIS	HD1	6.695

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	233	195	83.7
¹³C chemical shifts	171	64	37.4
¹⁵N chemical shifts	42	30	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	67	87.0
¹³C chemical shifts	76	34	44.7
¹⁵N chemical shifts	35	30	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	156	128	82.1
¹³C chemical shifts	95	30	31.6
¹⁵N chemical shifts	7	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	15	88.2
¹³C chemical shifts	17	1	5.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	17	77.3
¹³C chemical shifts	20	0	0.0
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 38, Sequence coverage: 94.7%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 33.3%
- Total number of restraints: 310
- Weight of restraints: 1.0 (310)
- Potential type of restraints: square-well-parabolic (310)
- Range of distance target values: 1.75, 6.0 (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

Keywords CDK, Nedd4L, signal transduction, SMAD

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Found 1 Document (1.896 seconds)

BMRB: 17538

Sample #1

Sample #2

Sample #3

Related entities 1. second WW domain from human YAP, : 398 entities Detail

Related entities 2. human Smad1 derived peptide, : 1 : 4 : 1 : 1 entities Detail

Interaction partners 1. second WW domain from human YAP, : 61 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail