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Found 1 Document (0.679 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)
2:3:GLU:C	2:4:TPO:N	unknown	unknown	n/a
2:4:TPO:C	2:5: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	assigned_chem_shift_list_1	Warning	358		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: 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: 251
  - 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
25	ARG	HH21	5.881
31	HIS	HD1	6.751
33	THR	HG1	4.842

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	232	216	93.1
¹³C chemical shifts	164	65	39.6
¹⁵N chemical shifts	43	42	97.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	70	97.2
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	10	10	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	48	29	60.4
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	8	61.5
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	35	21	60.0
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 (0.679 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