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Found 1 Document (2.212 seconds)

BMRB: 17539

2LAX

Structure of first WW domain of human YAP in complex with a human Smad1 doubly-phosphorylated derived peptide.

Authors

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

Assembly

first WW domain of human YAP in complex with a human Smad1 doubly-phosphorilated derived peptide

Entity

1. first WW domain of human YAP (polymer, Thiol state: not present), 40 monomers, 4534.991 Da Detail

GAMEDVPLPA GWEMAKTSSG QRYFLNHIDQ TTTWQDPRKA

2. Smad1 doubly-phosphorilated derived peptide (polymer, Thiol state: not present), 9 monomers, 1135.957 Da Detail

SXYPHXPTS

Total weight

5670.948 Da

Max. entity weight

4534.991 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 73.5 %, Completeness: 70.5 %, Completeness (bb): 75.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	70.5 % (198 of 281)	70.5 % (198 of 281)
Backbone	75.0 % (69 of 92)	75.0 % (69 of 92)
Sidechain	68.3 % (129 of 189)	68.3 % (129 of 189)
Aromatic	62.1 % (18 of 29)	62.1 % (18 of 29)
Methyl	88.2 % (15 of 17)	88.2 % (15 of 17)

1. first WW domain of human YAP

GAMEDVPLPA GWEMAKTSSG QRYFLNHIDQ TTTWQDPRKA

2. Smad1 doubly-phosphorilated derived peptide

SXYPHXPTS

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: 2LAX, 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. first WW domain of human YAP, : 290 entities Detail

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_17539_2lax.nef
Input source #2: Coordindates	2lax.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)
B:201:SER:C	B:202:TPO:N	unknown	unknown	n/a
B:202:TPO:C	B:203:TYR:N	unknown	unknown	n/a
B:205:HIS:C	B:206:SEP:N	unknown	unknown	n/a
B:206:SEP:C	B:207:PRO:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	202	TPO	PHOSPHOTHREONINE	Coordinates
B	206	SEP	PHOSPHOSERINE	Coordinates

Sequence alignments

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

--170-------180-------190-------200-----
GAMEDVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQDPRKA
||||||||||||||||||||||||||||||||||||||||
GAMEDVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQDPRKA
--------10--------20--------30--------40

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

---------
SXYPHXPTS
|||||||||
SXYPHXPTS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	40	0	0	100.0
B	B	9	0	0	100.0

Content subtype: combined_17539_2lax.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	nef_chemical_shift_list_assigned_chem_shift_list_1	Warning	201		90.0 (chain: A, length: 40)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	275 (1)	noe	97.5 (chain: A, length: 40)

Assigned chemical shifts

Saveframe: nef_chemical_shift_list_assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 90.0%
- Total number of assignments
  - ¹H chemical shifts: 201
- Completeness of assignments
  - Entity_assemble_ID: A
- 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)
182	THR	HG1	4.762
192	HIS	HD1	6.592

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	241	197	81.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	69	86.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	128	79.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	15	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	18	78.3

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 97.5%
- Total number of restraints: 275
- Weight of restraints: 1.0 (275)
- Potential type of restraints: square-well-parabolic (275)
- Range of distance target values: 1.75, 5.58 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords CDK, signal transduction, SMAD, YAP

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Found 1 Document (2.212 seconds)

BMRB: 17539

Sample #1

Sample #2

Sample #3

Related entities 1. first WW domain of human YAP, : 290 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail