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BMRB: 17543

2LB1

Structure of the second domain of human Smurf1 in complex with a human Smad1 derived peptide containing a PY motif

Authors

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

Assembly

first domain of human Smurf1 in complex with a human Smad1 derived peptide

Entity

1. human Smurf1 (polymer, Thiol state: not present), 35 monomers, 4027.459 Da Detail

LGPLPPGWEV RSTVSGRIYF VDHNNRTTQF TDPRL

2. human Smad1 derived peptide (polymer, Thiol state: not present), 13 monomers, 1408.506 Da Detail

DTPPPAYLPP EDP

Total weight

5435.965 Da

Max. entity weight

4027.459 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.9 %, Completeness: 57.4 %, Completeness (bb): 57.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	57.4 % (321 of 559)	86.4 % (254 of 294)	21.5 % (48 of 223)	45.2 % (19 of 42)
Backbone	57.1 % (153 of 268)	96.6 % (86 of 89)	34.0 % (48 of 141)	50.0 % (19 of 38)
Sidechain	56.5 % (190 of 336)	82.0 % (168 of 205)	17.3 % (22 of 127)	0.0 % (0 of 4)
Aromatic	32.7 % (17 of 52)	65.4 % (17 of 26)	0.0 % (0 of 25)	0.0 % (0 of 1)
Methyl	50.0 % (22 of 44)	95.5 % (21 of 22)	4.5 % (1 of 22)

1. human Smurf1

LGPLPPGWEV RSTVSGRIYF VDHNNRTTQF TDPRL

2. human Smad1 derived peptide

DTPPPAYLPP EDP

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	Smurf1	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	Smurf1	[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	Smurf1	[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 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LB1, 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 Smurf1, : 5 : 1 : 429 entities Detail

Related entities 2. human Smad1 derived peptide, : 1 : 7 : 2 : 1 : 4 entities Detail

Interaction partners 1. human Smurf1, : 5 interactors Detail

More details for 5 interactors identified by 4 citations

Interaction partners 2. human Smad1 derived peptide, : 6 interactors Detail

More details for 6 interactors identified by 4 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	Smurf1	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	Smurf1	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	Smurf1	[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	Smurf1	[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	Smurf1	[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_17543_2lb1.nef
Input source #2: Coordindates	2lb1.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)
2:14:PRO:C	2:15:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	234	NH2	AMINO GROUP	Coordinates

Sequence alignments

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

-280-----290-------300-------310----
LGPLPPGWEVRSTVSGRIYFVDHNNRTTQFTDPRLH
||||||||||||||||||||||||||||||||||||
LGPLPPGWEVRSTVSGRIYFVDHNNRTTQFTDPRLH
--------10--------20--------30------

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

220-----230----
ADTPPPAYLPPEDPX
|||||||||||||||
ADTPPPAYLPPEDPX
--------10-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	36	0	0	100.0
B	B	15	0	0	100.0

Content subtype: combined_17543_2lb1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	316		97.2 (chain: A, length: 36), 80.0 (chain: B, length: 15)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	283 (1)	noe	97.2 (chain: A, length: 36), 46.7 (chain: B, length: 15)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 97.2%
  - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 80.0%
- Total number of assignments
  - ¹H chemical shifts: 255
  - ¹³C chemical shifts: 44
  - ¹⁵N chemical shifts: 17
- 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)
301	HIS	HD1	7.144

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	222	190	85.6
¹³C chemical shifts	168	44	26.2
¹⁵N chemical shifts	40	17	42.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	68	95.8
¹³C chemical shifts	72	24	33.3
¹⁵N chemical shifts	32	17	53.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	151	122	80.8
¹³C chemical shifts	96	20	20.8
¹⁵N chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	18	100.0
¹³C chemical shifts	18	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	15	62.5
¹³C chemical shifts	23	0	0.0
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	62	74.7
¹³C chemical shifts	63	0	0.0
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	18	81.8
¹³C chemical shifts	28	0	0.0
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	44	72.1
¹³C chemical shifts	35	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	3	60.0
¹³C chemical shifts	5	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: 36, Sequence coverage: 97.2%
  - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 46.7%
- Total number of restraints: 283
- Weight of restraints: 1.0 (283)
- Potential type of restraints: square-well-parabolic (283)
- Range of distance target values: 1.75, 5.35 (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, SMURF

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Found 1 Document (0.809 seconds)

BMRB: 17543

Sample #1

Sample #2

Sample #3

Related entities 1. human Smurf1, : 5 : 1 : 429 entities Detail

Related entities 2. human Smad1 derived peptide, : 1 : 7 : 2 : 1 : 4 entities Detail

Interaction partners 1. human Smurf1, : 5 interactors Detail

Interaction partners 2. human Smad1 derived peptide, : 6 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail