BMRBj - BMREntryMaster

Found 1 Document (2.143 seconds)

BMRB: 17542

2LB0

Structure of the first domain of human Smurf1 in complex with a doubly phosphorylated human Smad1 derived peptide.

Authors

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

Assembly

human Smurf1 in complex with a doubly phosphorylated human Smad1 derived peptide

Entity

1. human Smurf1 (polymer, Thiol state: not present), 36 monomers, 4133.510 Da Detail

GAMELPEGYE QRTTVQGQVY FLHTQTGVST WHDPRI

2. doubly phosphorylated human Smad1 derived peptide (polymer, Thiol state: not present), 10 monomers, 1181.981 Da Detail

TSXDPGXPFQ

Total weight

5315.4907 Da

Max. entity weight

4133.51 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 71.7 %, Completeness: 52.4 %, Completeness (bb): 53.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	52.4 % (264 of 504)	73.6 % (192 of 261)	26.4 % (52 of 197)	43.5 % (20 of 46)
Backbone	53.5 % (137 of 256)	75.3 % (67 of 89)	39.4 % (50 of 127)	50.0 % (20 of 40)
Sidechain	52.3 % (150 of 287)	72.7 % (125 of 172)	22.9 % (25 of 109)	0.0 % (0 of 6)
Aromatic	28.6 % (16 of 56)	57.1 % (16 of 28)	0.0 % (0 of 27)	0.0 % (0 of 1)
Methyl	44.7 % (17 of 38)	89.5 % (17 of 19)	0.0 % (0 of 19)

1. human Smurf1

GAMELPEGYE QRTTVQGQVY FLHTQTGVST WHDPRI

2. doubly phosphorylated human Smad1 derived peptide

TSXDPGXPFQ

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 21 models in PDB: 2LB0, 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 : 348 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	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_17542_2lb0.nef
Input source #2: Coordindates	2lb0.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:209:SER:C	B:210:SEP:N	unknown	unknown	n/a
B:210:SEP:C	B:211:ASP:N	unknown	unknown	n/a
B:213:GLY:C	B:214:SEP:N	unknown	unknown	n/a
B:214:SEP:C	B:215:PRO:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	210	SEP	PHOSPHOSERINE	Coordinates
B	214	SEP	PHOSPHOSERINE	Coordinates

Sequence alignments

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

------240-------250-------260-------
GAMELPEGYEQRTTVQGQVYFLHTQTGVSTWHDPRI
||||||||||||||||||||||||||||||||||||
GAMELPEGYEQRTTVQGQVYFLHTQTGVSTWHDPRI
--------10--------20--------30------

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

--210-----
TSXDPGXPFQ
||||||||||
TSXDPGXPFQ
--------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	10	0	0	100.0

Content subtype: combined_17542_2lb0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	nef_chemical_shift_list_assigned_chem_shift_list_1	Warning	261		91.7 (chain: A, length: 36)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	360 (1)	noe	94.4 (chain: A, length: 36)

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: 91.7%
- Total number of assignments
  - ¹H chemical shifts: 193
  - ¹³C chemical shifts: 49
  - ¹⁵N chemical shifts: 19
- 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)
254	HIS	HD1	5.793
263	HIS	HD1	7.097

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	215	191	88.8
¹³C chemical shifts	163	49	30.1
¹⁵N chemical shifts	39	19	48.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	67	90.5
¹³C chemical shifts	72	26	36.1
¹⁵N chemical shifts	34	19	55.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	141	124	87.9
¹³C chemical shifts	91	23	25.3
¹⁵N chemical shifts	5	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	17	89.5
¹³C chemical shifts	19	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	16	69.6
¹³C chemical shifts	22	0	0.0
¹⁵N chemical shifts	1	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: 94.4%
- Total number of restraints: 360
- Weight of restraints: 1.0 (360)
- Potential type of restraints: square-well-parabolic (360)
- Range of distance target values: 1.77, 4.91 (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, signal transduction, SMAD, SMURF

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (2.143 seconds)

BMRB: 17542

Sample #1

Sample #2

Sample #3

Related entities 1. human Smurf1, : 5 : 348 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail