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Found 1 Document (2.057 seconds)

BMRB: 17545

2LB3

Structure of the first domain of human PIN1 in complex with a human Smad3 derived peptide.

Authors

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

Assembly

first domain of human PIN1 in complex with a human Smad3 derived peptide( resi 173-186)

Entity

1. first domain of human PIN1 (polymer, Thiol state: not present), 36 monomers, 4224.635 Da Detail

KLPPGWEKRM SRSSGRVYYF NHITNASQWE RPSGNS

2. human Smad3 derived peptide (polymer, Thiol state: not present), 8 monomers, 886.8810 Da Detail

IPEXPPPG

Total weight

5111.5156 Da

Max. entity weight

4224.635 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.5 %, Completeness: 68.5 %, Completeness (bb): 72.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	68.5 % (352 of 514)	89.1 % (246 of 276)	34.7 % (68 of 196)	90.5 % (38 of 42)
Backbone	72.1 % (176 of 244)	95.2 % (79 of 83)	52.0 % (65 of 125)	88.9 % (32 of 36)
Sidechain	67.0 % (207 of 309)	86.5 % (167 of 193)	30.9 % (34 of 110)	100.0 % (6 of 6)
Aromatic	53.7 % (29 of 54)	100.0 % (27 of 27)	0.0 % (0 of 25)	100.0 % (2 of 2)
Methyl	60.0 % (12 of 20)	90.0 % (9 of 10)	30.0 % (3 of 10)

1. first domain of human PIN1

KLPPGWEKRM SRSSGRVYYF NHITNASQWE RPSGNS

2. human Smad3 derived peptide

IPEXPPPG

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	PIN1	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	PIN1	[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	PIN1	[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 20 models in PDB: 2LB3, 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. first domain of human PIN1, : 1 : 3 : 181 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	PIN1	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	PIN1	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	PIN1	[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	PIN1	[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	PIN1	[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_17545_2lb3.nef
Input source #2: Coordindates	2lb3.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

10-------20--------30--------40-----
KLPPGWEKRMSRSSGRVYYFNHITNASQWERPSGNS
||||||||||||||||||||||||||||||||||||
KLPPGWEKRMSRSSGRVYYFNHITNASQWERPSGNS
--------10--------20--------30------

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

--180---
IPEXPPPG
||||||||
IPEXPPPG
--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	36	0	0	100.0
B	B	8	0	0	100.0

Content subtype: combined_17545_2lb3.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	352		100.0 (chain: A, length: 36), 87.5 (chain: B, length: 8)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	200 (1)	noe	80.6 (chain: A, length: 36), 12.5 (chain: B, length: 8)

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: 100.0%
  - Entity_assembly_ID: B, Chain length: 8, Sequence coverage: 87.5%
- Total number of assignments
  - ¹H chemical shifts: 245
  - ¹³C chemical shifts: 65
  - ¹⁵N chemical shifts: 42
- 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)
18	ARG	HH21	6.213
18	ARG	NE	112.604
21	ARG	NE	115.299
25	ARG	HH21	5.881
25	ARG	NE	114.165
31	HIS	HD1	6.751
33	THR	HG1	4.842
40	ARG	NE	115.597

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	232	217	93.5
¹³C chemical shifts	164	65	39.6
¹⁵N chemical shifts	39	38	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	71	98.6
¹³C chemical shifts	72	34	47.2
¹⁵N chemical shifts	33	32	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	160	146	91.2
¹³C chemical shifts	92	31	33.7
¹⁵N chemical shifts	6	6	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	8	88.9
¹³C chemical shifts	9	1	11.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	27	100.0
¹³C chemical shifts	25	0	0.0
¹⁵N chemical shifts	2	2	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	30	63.8
¹³C chemical shifts	36	0	0.0
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	9	69.2
¹³C chemical shifts	16	0	0.0
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	21	61.8
¹³C chemical shifts	20	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	1	33.3
¹³C chemical shifts	3	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 80.6%
  - Entity_assembly_ID: B, Chain length: 8, Sequence coverage: 12.5%
- Total number of restraints: 200
- Weight of restraints: 1.0 (200)
- Potential type of restraints: square-well-parabolic (200)
- Range of distance target values: 1.75, 5.39 (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, PIN1, signal transduction, SMAD

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Found 1 Document (2.057 seconds)

BMRB: 17545

Sample #1

Sample #2

Sample #3

Related entities 1. first domain of human PIN1, : 1 : 3 : 181 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail