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BMRB: 18501

2LTY

NEDD4L WW2 domain in complex with a Smad7 derived peptide.

Authors

Macias, M.J., Aragon, E., Goerner, N., Xi, Q., Lopes, T., Gao, S., Massague, J.

Assembly

NEDD4L WW2 domain in complex with a Smad7 derived peptide

Entity

1. NEDD4LWW2 (polymer, Thiol state: not present), 34 monomers, 3959.302 Da Detail

PGLPSGWEER KDAKGRTYYV NHNNRTTTWT RPIG

2. SMAD7 (polymer, Thiol state: not present), 15 monomers, 1777.946 Da Detail

ELESPPPPYS RYPMD

Total weight

5737.248 Da

Max. entity weight

3959.302 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 69.4 %, Completeness: 65.7 %, Completeness (bb): 73.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	65.7 % (203 of 309)	65.7 % (203 of 309)
Backbone	73.4 % (69 of 94)	73.4 % (69 of 94)
Sidechain	62.3 % (134 of 215)	62.3 % (134 of 215)
Aromatic	60.0 % (18 of 30)	60.0 % (18 of 30)
Methyl	85.7 % (12 of 14)	85.7 % (12 of 14)

1. NEDD4LWW2

PGLPSGWEER KDAKGRTYYV NHNNRTTTWT RPIG

2. SMAD7

ELESPPPPYS RYPMD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	NEDD4LWW2	natural abundance	1 mM
2	SMAD7	natural abundance	2 mM
3	TRIS	[U-100% 2H]	20 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7.2

#	Name	Isotope labeling	Concentration
7	NEDD4LWW2	[U-100% 13C; U-100% 15N]	1 mM
8	SMAD7	natural abundance	3 mM
9	TRIS	[U-100% 2H]	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Chem. Shift Complete2

Sequence coverage: 34.7 %, Completeness: 49.8 %, Completeness (bb): 52.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	49.8 % (308 of 618)	49.8 % (308 of 618)
Backbone	52.1 % (98 of 188)	52.1 % (98 of 188)
Sidechain	48.8 % (210 of 430)	48.8 % (210 of 430)
Aromatic	43.3 % (26 of 60)	43.3 % (26 of 60)
Methyl	42.9 % (12 of 28)	42.9 % (12 of 28)

1. NEDD4LWW2

PGLPSGWEER KDAKGRTYYV NHNNRTTTWT RPIG

2. SMAD7

ELESPPPPYS RYPMD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	NEDD4LWW2	natural abundance	1 mM
2	SMAD7	natural abundance	2 mM
3	TRIS	[U-100% 2H]	20 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 7.2

#	Name	Isotope labeling	Concentration
7	NEDD4LWW2	[U-100% 13C; U-100% 15N]	1 mM
8	SMAD7	natural abundance	3 mM
9	TRIS	[U-100% 2H]	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Protein Blocks Logo

Calculated from 30 models in PDB: 2LTY, Strand ID: A, B Detail

Release date

2012-11-18

Citation

Structural basis for the versatile interactions of Smad7 with regulator WW domains in TGF-β Pathways
Aragon, E., Goerner, N., Xi, Q., Gomes, T., Gao, S., Massague, J., Macias, M.J.
Structure (2012), 20, 1726-1736, PubMed 22921829 , DOI 10.1016/j.str.2012.07.014 , Abstract

Related entities 1. NEDD4LWW2, : 6 : 429 entities Detail

Related entities 2. SMAD7, : 1 : 10 entities Detail

Interaction partners 1. NEDD4LWW2, : 10 interactors Detail

More details for 10 interactors identified by 4 citations

Interaction partners 2. SMAD7, : 11 interactors Detail

More details for 11 interactors identified by 7 citations

Experiments performed 5 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18501_2lty.nef
Input source #2: Coordindates	2lty.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

---370-------380-------390--------
PGLPSGWEERKDAKGRTYYVNHNNRTTTWTRPIG
||||||||||||||||||||||||||||||||||
PGLPSGWEERKDAKGRTYYVNHNNRTTTWTRPIG
--------10--------20--------30----

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

-----210-------
ELESPPPPYSRYPMD
|||||||||||||||
ELESPPPPYSRYPMD
--------10-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	34	0	0	100.0
B	B	15	0	0	100.0

Content subtype: combined_18501_2lty.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	NEDD4LWW21	Warning	210		100.0 (chain: A, length: 34)
2	Assigned chemical shifts	SMAD71	Warning	93		100.0 (chain: B, length: 15)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	558 (1)	noe	100.0 (chain: A, length: 34), 100.0 (chain: B, length: 15)

Assigned chemical shifts

Saveframe: NEDD4LWW21
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 210
- 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
Saveframe: SMAD71
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 93
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
389	ARG	HH11	7.404
389	ARG	HH12	7.404
389	ARG	HH22	6.704
390	THR	HG1	5.642
395	ARG	HH11	6.635
395	ARG	HH12	6.635
395	ARG	HH22	6.673

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	211	203	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	69	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	142	134	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	12	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	18	81.8

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
203	GLU	HE2	7.786

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	92	93.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	24	96.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	68	93.2

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 100.0%
- Total number of restraints: 558
- Weight of restraints: 1.0 (558)
- Potential type of restraints: square-well-parabolic (558)
- 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 NEDD4L, SMAD7, WW

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Found 1 Document (1.25 seconds)

BMRB: 18501

Sample #1

Sample #2

Sample #1

Sample #2

Related entities 1. NEDD4LWW2, : 6 : 429 entities Detail

Related entities 2. SMAD7, : 1 : 10 entities Detail

Interaction partners 1. NEDD4LWW2, : 10 interactors Detail

Interaction partners 2. SMAD7, : 11 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail