BMRBj - BMREntryMaster

Found 1 Document (0.541 seconds)

BMRB: 17529

2LAJ

Third WW domain of human Nedd4L in complex with doubly phosphorylated human smad3 derived peptide.

Authors

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

Assembly

Nedd4LW3/smad3 complex

Entity

1. NEDD4LWW3 (polymer, Thiol state: not present), 44 monomers, 5203.819 Da Detail

GAMEQSFLPP GWEMRIAPNG RPFFYDHNTK TTTWEDPRLK FPVH

2. SMAD3 (polymer, Thiol state: not present), 10 monomers, 1112.965 Da Detail

AGXPNLXPNP

Total weight

6316.7837 Da

Max. entity weight

5203.819 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.0 %, Completeness: 56.5 %, Completeness (bb): 57.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	56.5 % (355 of 628)	80.1 % (266 of 332)	27.2 % (67 of 246)	44.0 % (22 of 50)
Backbone	57.8 % (170 of 294)	85.9 % (85 of 99)	41.4 % (63 of 152)	51.2 % (22 of 43)
Sidechain	56.0 % (214 of 382)	77.7 % (181 of 233)	23.2 % (33 of 142)	0.0 % (0 of 7)
Aromatic	50.0 % (40 of 80)	100.0 % (40 of 40)	0.0 % (0 of 38)	0.0 % (0 of 2)
Methyl	2.9 % (1 of 34)	0.0 % (0 of 17)	5.9 % (1 of 17)

1. NEDD4LWW3

GAMEQSFLPP GWEMRIAPNG RPFFYDHNTK TTTWEDPRLK FPVH

2. SMAD3

AGXPNLXPNP

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 15 models in PDB: 2LAJ, 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. NEDD4LWW3, : 6 : 120 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_17529_2laj.nef
Input source #2: Coordindates	2laj.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)
2:2:GLY:C	2:3:SEP:N	unknown	unknown	n/a
2:3:SEP:C	2:4:PRO:N	unknown	unknown	n/a
2:6:LEU:C	2:7:SEP:N	unknown	unknown	n/a
2:7:SEP:C	2:8:PRO:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	204	SEP	PHOSPHOSERINE	Assigned chemical shifts, Coordinates
B	208	SEP	PHOSPHOSERINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

------480-------490-------500-------510-----
GAMEQSFLPPGWEMRIAPNGRPFFYDHNTKTTTWEDPRLKFPVH
||||||||||||||||||||||||||||||||||||||||||||
GAMEQSFLPPGWEMRIAPNGRPFFYDHNTKTTTWEDPRLKFPVH
--------10--------20--------30--------40----

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

------210-
AGXPNLXPNP
||||||||||
AGXPNLXPNP
--------10

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	44	0	0	100.0
B	B	10	0	0	100.0

Content subtype: combined_17529_2laj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	359		90.9 (chain: A, length: 44), 90.0 (chain: B, length: 10)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	380 (1)	noe	97.7 (chain: A, length: 44)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 90.9%
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 90.0%
- Total number of assignments
  - ¹H chemical shifts: 276
  - ¹³C chemical shifts: 61
  - ¹⁵N chemical shifts: 22
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
515	HIS	HD1	6.525

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	286	246	86.0
¹³C chemical shifts	214	61	28.5
¹⁵N chemical shifts	46	22	47.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	85	76	89.4
¹³C chemical shifts	88	32	36.4
¹⁵N chemical shifts	38	22	57.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	201	170	84.6
¹³C chemical shifts	126	29	23.0
¹⁵N chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	0	0.0
¹³C chemical shifts	16	1	6.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	40	100.0
¹³C chemical shifts	38	0	0.0
¹⁵N chemical shifts	2	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	28	51.9
¹³C chemical shifts	36	0	0.0
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	14	77.8
¹³C chemical shifts	18	0	0.0
¹⁵N chemical shifts	7	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	14	38.9
¹³C chemical shifts	18	0	0.0
¹⁵N chemical shifts	2	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	0	0.0
¹³C chemical shifts	3	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: 44, Sequence coverage: 97.7%
- Total number of restraints: 380
- Weight of restraints: 1.0 (380)
- Potential type of restraints: square-well-parabolic (380)
- 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
    None
- Distance restraints on contact map

Keywords CDK, Nedd4L, signal transduction, SMAD

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Found 1 Document (0.541 seconds)

BMRB: 17529

Sample #1

Sample #2

Sample #3

Related entities 1. NEDD4LWW3, : 6 : 120 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail