BMRBj - BMREntryMaster

Found 1 Document (2.119 seconds)

BMRB: 17540

2LAY

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

Authors

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

Assembly

human Yap in complex with a human Smad1 derived peptide

Entity

1. human Yap (polymer, Thiol state: not present), 36 monomers, 4146.552 Da Detail

DVPLPAGWEM AKTSSGQRYF LNHIDQTTTW QDPRKA

2. human Smad1 derived peptide (polymer, Thiol state: not present), 9 monomers, 1055.977 Da Detail

STYPHXPTS

Total weight

5202.529 Da

Max. entity weight

4146.552 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 80.0 %, Completeness: 58.5 %, Completeness (bb): 65.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	58.5 % (299 of 511)	75.6 % (201 of 266)	34.5 % (69 of 200)	64.4 % (29 of 45)
Backbone	65.0 % (165 of 254)	83.5 % (71 of 85)	50.0 % (65 of 130)	74.4 % (29 of 39)
Sidechain	55.2 % (165 of 299)	71.8 % (130 of 181)	31.3 % (35 of 112)	0.0 % (0 of 6)
Aromatic	31.0 % (18 of 58)	62.1 % (18 of 29)	0.0 % (0 of 27)	0.0 % (0 of 2)
Methyl	61.8 % (21 of 34)	88.2 % (15 of 17)	35.3 % (6 of 17)

1. human Yap

DVPLPAGWEM AKTSSGQRYF LNHIDQTTTW QDPRKA

2. human Smad1 derived peptide

STYPHXPTS

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	SMAD1	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	SMAD1	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	SMAD1	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 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 2.39 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 2.39 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.16 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LAY, 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. human Yap, : 2 : 5 : 433 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	SMAD1	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	SMAD1	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	SMAD1	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	SMAD1	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	SMAD1	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_17540_2lay.nef
Input source #2: Coordindates	2lay.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: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	206	SEP	PHOSPHOSERINE	Coordinates

Sequence alignments

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

170-----180-------190-------200-----
DVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQDPRKA
||||||||||||||||||||||||||||||||||||
DVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQDPRKA
--------10--------20--------30------

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

---------
STYPHXPTS
|||||||||
STYPHXPTS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	36	0	0	100.0
B	B	9	0	0	100.0

Content subtype: combined_17540_2lay.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	nef_chemical_shift_list_assigned_chem_shift_list_1	Warning	293		100.0 (chain: A, length: 36)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	243 (1)	noe	88.9 (chain: A, length: 36), 44.4 (chain: B, length: 9)

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: 36, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 203
  - ¹³C chemical shifts: 62
  - ¹⁵N chemical shifts: 28
- 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)
182	THR	HG1	4.762
192	HIS	HD1	6.592

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	222	199	89.6
¹³C chemical shifts	164	62	37.8
¹⁵N chemical shifts	39	28	71.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	71	100.0
¹³C chemical shifts	72	31	43.1
¹⁵N chemical shifts	33	28	84.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	151	128	84.8
¹³C chemical shifts	92	31	33.7
¹⁵N chemical shifts	6	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	15	93.8
¹³C chemical shifts	16	3	18.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	18	78.3
¹³C chemical shifts	21	0	0.0
¹⁵N chemical shifts	2	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 88.9%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 44.4%
- Total number of restraints: 243
- Weight of restraints: 1.0 (243)
- Potential type of restraints: square-well-parabolic (243)
- Range of distance target values: 3.19, 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
- Distance restraints on contact map

Keywords CDK, signal transduction, SMAD, YAP

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Found 1 Document (2.119 seconds)

BMRB: 17540

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. human Yap, : 2 : 5 : 433 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail