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Found 1 Document (2.519 seconds)

BMRB: 17544

2LB2

Structure of the second domain of human Nedd4L in complex with a doubly phosphorylated human Smad3 derived peptide.

Authors

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

Assembly

second domain of human Nedd4L in complex with a doubly phosphorylated human Smad3 (res 178-189) derived peptide

Entity

1. second domain of human Nedd4L (polymer, Thiol state: not present), 35 monomers, 4177.618 Da Detail

GLPSGWEERK DAKGRTYYVN HNNRTTTWTR PIMQL

2. doubly phosphorylated human Smad3 (polymer, Thiol state: not present), 12 monomers, 1341.271 Da Detail

EXPPPGYLSE DG

Total weight

5518.889 Da

Max. entity weight

4177.618 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.7 %, Completeness: 74.6 %, Completeness (bb): 71.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.6 % (402 of 539)	93.0 % (265 of 285)	49.8 % (103 of 207)	72.3 % (34 of 47)
Backbone	71.4 % (190 of 266)	93.5 % (86 of 92)	52.6 % (70 of 133)	82.9 % (34 of 41)
Sidechain	77.7 % (244 of 314)	92.7 % (179 of 193)	56.5 % (65 of 115)	0.0 % (0 of 6)
Aromatic	40.4 % (21 of 52)	80.8 % (21 of 26)	0.0 % (0 of 24)	0.0 % (0 of 2)
Methyl	84.4 % (27 of 32)	100.0 % (16 of 16)	68.8 % (11 of 16)

1. second domain of human Nedd4L

GLPSGWEERK DAKGRTYYVN HNNRTTTWTR PIMQL

2. doubly phosphorylated human Smad3

EXPPPGYLSE DG

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	Nedd4L	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	Nedd4L	[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	Nedd4L	[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 25 models in PDB: 2LB2, 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 domain of human Nedd4L, : 6 : 432 entities Detail

Related entities 2. doubly phosphorylated human Smad3, : 1 : 6 : 12 entities Detail

Interaction partners 1. second domain of human Nedd4L, : 10 interactors Detail

More details for 10 interactors identified by 4 citations

Interaction partners 2. doubly phosphorylated human Smad3, : 129 : 1 interactors Detail

More details for 130 interactors identified by 33 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	Nedd4L	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	Nedd4L	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	Nedd4L	[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	Nedd4L	[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	Nedd4L	[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_17544_2lb2.nef
Input source #2: Coordindates	2lb2.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:178:GLU:C	B:179:TPO:N	unknown	unknown	n/a
B:179:TPO:C	B:180:PRO:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	179	TPO	PHOSPHOTHREONINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

--370-------380-------390-------400
GLPSGWEERKDAKGRTYYVNHNNRTTTWTRPIMQL
|||||||||||||||||||||||||||||||||||
GLPSGWEERKDAKGRTYYVNHNNRTTTWTRPIMQL
--------10--------20--------30-----

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

--180-------
EXPPPGYLSEDG
||||||||||||
EXPPPGYLSEDG
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	35	0	0	100.0
B	B	12	0	0	100.0

Content subtype: combined_17544_2lb2.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	410		100.0 (chain: A, length: 35), 91.7 (chain: B, length: 12)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	397 (1)	noe	100.0 (chain: A, length: 35), 41.7 (chain: B, length: 12)

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: 35, Sequence coverage: 100.0%

--370-------380-------390-------400
GLPSGWEERKDAKGRTYYVNHNNRTTTWTRPIMQL
|||||||||||||||||||||||||||||||||||
GLPSGWEERKDAKGRTYYVNHNNRTTTWTRPIMQL

Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 91.7%

--180-------
EXPPPGYLSEDG
||||||||||| 
EXPPPGYLSED 
--180------

Total number of assignments
- ¹H chemical shifts: 279
- ¹³C chemical shifts: 98
- ¹⁵N chemical shifts: 33

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
380	ARG	HH21	6.586
380	ARG	HH22	7.155
386	HIS	HD1	6.276
389	ARG	HH11	7.336
389	ARG	HH12	7.336
389	ARG	HH22	6.655
390	THR	HG1	5.647
391	THR	HG1	4.852
395	ARG	HH11	6.636
395	ARG	HH12	6.636
395	ARG	HH21	6.324
395	ARG	HH22	6.694

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	223	213	95.5
¹³C chemical shifts	161	98	60.9
¹⁵N chemical shifts	39	33	84.6

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	70	98.6
¹³C chemical shifts	70	35	50.0
¹⁵N chemical shifts	33	33	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	152	143	94.1
¹³C chemical shifts	91	63	69.2
¹⁵N chemical shifts	6	0	0.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	14	93.3
¹³C chemical shifts	15	11	73.3

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	19	86.4
¹³C chemical shifts	20	0	0.0
¹⁵N chemical shifts	2	0	0.0

Entity_assemble_ID: B

Peptide bond of PRO
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	65	56	86.2
¹³C chemical shifts	50	0	0.0
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	18	78.3
¹³C chemical shifts	24	0	0.0
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	38	90.5
¹³C chemical shifts	26	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	2	66.7
¹³C chemical shifts	3	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	2	50.0
¹³C chemical shifts	4	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: 35, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 41.7%
- Total number of restraints: 395
- Weight of restraints: 1.0 (395)
- Potential type of restraints: square-well-parabolic (395)
- 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 (2.519 seconds)

BMRB: 17544

Sample #1

Sample #2

Sample #3

Related entities 1. second domain of human Nedd4L, : 6 : 432 entities Detail

Related entities 2. doubly phosphorylated human Smad3, : 1 : 6 : 12 entities Detail

Interaction partners 1. second domain of human Nedd4L, : 10 interactors Detail

Interaction partners 2. doubly phosphorylated human Smad3, : 129 : 1 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail