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BMRB: 16923

2KXQ

Solution Structure of Smurf2 WW2 and WW3 bound to Smad7 PY peptide Smad7 PY motif containing peptide

Authors

Chong, A., Lin, H., Wrana, J., Forman-Kay, J.D.

Assembly

Smurf2 WW2 and WW3 bound to Smad7 PY

Entity

1. WW23 (polymer, Thiol state: all free), 90 monomers, 10103.92 Da Detail

GPLGGSPPDL PEGYEQRTTQ QGQVYFLHTQ TGVSTWHDPR VPRDLSNINC EELGPLPPGW EIRNTATGRV YFVDHNNRTT QFTDPRLSAN

2. S7PY (polymer, Thiol state: not present), 20 monomers, 2189.400 Da Detail

GPLGSELESP PPPYSRYPMD

Total weight

12293.32 Da

Max. entity weight

10103.92 Da

Source organism

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.0 %, Completeness (bb): 83.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.0 % (1115 of 1253)	95.0 % (626 of 659)	78.8 % (383 of 486)	98.1 % (106 of 108)
Backbone	83.0 % (521 of 628)	95.8 % (206 of 215)	69.9 % (223 of 319)	97.9 % (92 of 94)
Sidechain	95.7 % (693 of 724)	94.6 % (420 of 444)	97.4 % (259 of 266)	100.0 % (14 of 14)
Aromatic	95.3 % (101 of 106)	96.2 % (51 of 53)	94.1 % (48 of 51)	100.0 % (2 of 2)
Methyl	100.0 % (88 of 88)	100.0 % (44 of 44)	100.0 % (44 of 44)

1. WW23

GPLGGSPPDL PEGYEQRTTQ QGQVYFLHTQ TGVSTWHDPR VPRDLSNINC EELGPLPPGW EIRNTATGRV YFVDHNNRTT QFTDPRLSAN

2. S7PY

GPLGSELESP PPPYSRYPMD

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	WW23	[U-100% 13C; U-100% 15N]		1.2 mM
2	S7PY	[U-100% 13C; U-100% 15N]		1.2 mM
3	NaCl	natural abundance		20 mM
4	NaPi	natural abundance		40 mM
5	EDTA	natural abundance		1 mM
6	NaAzide	natural abundance		0.05 %
7	Benzamidine	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2KXQ, Strand ID: A, B Detail

Release date

2010-10-13

Citation

Coupling of tandem Smad ubiquitination regulatory factor (Smurf) WW domains modulates target specificity
Chong, P., Lin, H., Wrana, J.L., Forman-Kay, J.D.
Proc. Natl. Acad. Sci. U. S. A. (2010), 107, 18404-18409, PubMed 20937913 , DOI 10.1073/pnas.1003023107 , Abstract

Related entities 1. WW23, : 207 entities Detail

Related entities 2. S7PY, : 1 : 1 : 1 entities Detail

Interaction partners 1. WW23, : 76 interactors Detail

More details for 76 interactors identified by 13 citations

Experiments performed 8 experiments Detail

1 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	WW23	[U-100% 13C; U-100% 15N]		1.2 mM
2	S7PY	[U-100% 13C; U-100% 15N]		1.2 mM
3	NaCl	natural abundance		20 mM
4	NaPi	natural abundance		40 mM
5	EDTA	natural abundance		1 mM
6	NaAzide	natural abundance		0.05 %
7	Benzamidine	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

2 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	WW23	[U-100% 13C; U-100% 15N]		1.2 mM
2	S7PY	[U-100% 13C; U-100% 15N]		1.2 mM
3	NaCl	natural abundance		20 mM
4	NaPi	natural abundance		40 mM
5	EDTA	natural abundance		1 mM
6	NaAzide	natural abundance		0.05 %
7	Benzamidine	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

3 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	WW23	[U-100% 13C; U-100% 15N]		1.2 mM
2	S7PY	[U-100% 13C; U-100% 15N]		1.2 mM
3	NaCl	natural abundance		20 mM
4	NaPi	natural abundance		40 mM
5	EDTA	natural abundance		1 mM
6	NaAzide	natural abundance		0.05 %
7	Benzamidine	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

4 3D NC-NOESY (N and C simultaneous)

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	WW23	[U-100% 13C; U-100% 15N]		1.2 mM
2	S7PY	[U-100% 13C; U-100% 15N]		1.2 mM
3	NaCl	natural abundance		20 mM
4	NaPi	natural abundance		40 mM
5	EDTA	natural abundance		1 mM
6	NaAzide	natural abundance		0.05 %
7	Benzamidine	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

5 HACAN

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	WW23	[U-100% 13C; U-100% 15N]		1.2 mM
2	S7PY	[U-100% 13C; U-100% 15N]		1.2 mM
3	NaCl	natural abundance		20 mM
4	NaPi	natural abundance		40 mM
5	EDTA	natural abundance		1 mM
6	NaAzide	natural abundance		0.05 %
7	Benzamidine	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

6 3D CCC-TOCSY-NNH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	WW23	[U-100% 13C; U-100% 15N]		1.2 mM
2	S7PY	[U-100% 13C; U-100% 15N]		1.2 mM
3	NaCl	natural abundance		20 mM
4	NaPi	natural abundance		40 mM
5	EDTA	natural abundance		1 mM
6	NaAzide	natural abundance		0.05 %
7	Benzamidine	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

7 HBCBCGCDHD_ARO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	WW23	[U-100% 13C; U-100% 15N]		1.2 mM
2	S7PY	[U-100% 13C; U-100% 15N]		1.2 mM
3	NaCl	natural abundance		20 mM
4	NaPi	natural abundance		40 mM
5	EDTA	natural abundance		1 mM
6	NaAzide	natural abundance		0.05 %
7	Benzamidine	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

8 HBCBCGCDCDHE_ARO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	WW23	[U-100% 13C; U-100% 15N]		1.2 mM
2	S7PY	[U-100% 13C; U-100% 15N]		1.2 mM
3	NaCl	natural abundance		20 mM
4	NaPi	natural abundance		40 mM
5	EDTA	natural abundance		1 mM
6	NaAzide	natural abundance		0.05 %
7	Benzamidine	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16923_2kxq.nef
Input source #2: Coordindates	2kxq.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

----250-------260-------270-------280-------290-------300-------310-------320-------330---
GPLGGSPPDLPEGYEQRTTQQGQVYFLHTQTGVSTWHDPRVPRDLSNINCEELGPLPPGWEIRNTATGRVYFVDHNNRTTQFTDPRLSAN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGGSPPDLPEGYEQRTTQQGQVYFLHTQTGVSTWHDPRVPRDLSNINCEELGPLPPGWEIRNTATGRVYFVDHNNRTTQFTDPRLSAN
--------10--------20--------30--------40--------50--------60--------70--------80--------90

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

--200-----210-------
GPLGSELESPPPPYSRYPMD
||||||||||||||||||||
GPLGSELESPPPPYSRYPMD
--------10--------20

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	90	0	0	100.0
B	B	20	0	0	100.0

Content subtype: combined_16923_2kxq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1131		100.0 (chain: A, length: 90), 100.0 (chain: B, length: 20)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	7079 (1)	noe	96.7 (chain: A, length: 90), 95.0 (chain: B, length: 20)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	14 (1)	noe	8.9 (chain: A, length: 90)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	112 (112)	.	83.3 (chain: A, length: 90), 45.0 (chain: B, length: 20)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	Warning	49 (49)	.	51.1 (chain: A, length: 90), 15.0 (chain: B, length: 20)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 100.0%

----250-------260-------270-------280-------290-------300-------310-------320-------330---
GPLGGSPPDLPEGYEQRTTQQGQVYFLHTQTGVSTWHDPRVPRDLSNINCEELGPLPPGWEIRNTATGRVYFVDHNNRTTQFTDPRLSAN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGGSPPDLPEGYEQRTTQQGQVYFLHTQTGVSTWHDPRVPRDLSNINCEELGPLPPGWEIRNTATGRVYFVDHNNRTTQFTDPRLSAN

Entity_assembly_ID: B, Chain length: 20, Sequence coverage: 100.0%

--200-----210-------
GPLGSELESPPPPYSRYPMD
||||||||||||||||||||
GPLGSELESPPPPYSRYPMD

Total number of assignments
- ¹H chemical shifts: 634
- ¹³C chemical shifts: 369
- ¹⁵N chemical shifts: 128

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
245	PRO	N	133.66
250	PRO	N	139.59
251	PRO	N	135.359
254	PRO	N	134.969
271	HIS	ND1	245.21
271	HIS	NE2	168.204
280	HIS	ND1	229.998
280	HIS	NE2	182.73
282	PRO	N	138.105
285	PRO	N	139.564
298	PRO	N	133.937
300	PRO	N	136.635
301	PRO	N	134.85
318	HIS	ND1	237.955
318	HIS	NE2	165.913
328	PRO	N	140.58

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	537	521	97.0
¹³C chemical shifts	396	301	76.0
¹⁵N chemical shifts	101	95	94.1

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	179	174	97.2
¹³C chemical shifts	180	90	50.0
¹⁵N chemical shifts	80	78	97.5

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	358	347	96.9
¹³C chemical shifts	216	211	97.7
¹⁵N chemical shifts	21	17	81.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	40	100.0
¹³C chemical shifts	40	40	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	42	93.3
¹³C chemical shifts	43	40	93.0
¹⁵N chemical shifts	2	2	100.0

Entity_assemble_ID: B

Redox state of CYS
Peptide bond of PRO
Tautomeric state of HIS
Rotameric state of ILE , LEU, and VAL
Histogram of normalized assigned chemical shifts
Random coil index and derived parameters (S² and NMR RMSD)
- Chain_ID: A
- Chain_ID: B

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 96.7%
  - Entity_assembly_ID: B, Chain length: 20, Sequence coverage: 95.0%
- Total number of restraints: 6688
- Weight of restraints: 1.0 (6688)
- Potential type of restraints: square-well-parabolic (6688)
- Range of distance target values: 1.9, 3.5 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 8.9%
  - Total number of restraints: 14
  - Weight of restraints: 1.0 (14)
  - Potential type of restraints: square-well-parabolic (14)
  - Range of distance target values: 3.5, 3.5 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 83.3%
  - Entity_assembly_ID: B, Chain length: 20, Sequence coverage: 45.0%
- Total number of restraints: 112
- Total number of restraints per polymer type: 112
- Weight of restraints: 1.0 (112)
- Potential type of restraints: square-well-parabolic (112)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: Warning
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 51.1%

----250-------260-------270-------280-------290-------300-------310-------320-------330---
GPLGGSPPDLPEGYEQRTTQQGQVYFLHTQTGVSTWHDPRVPRDLSNINCEELGPLPPGWEIRNTATGRVYFVDHNNRTTQFTDPRLSAN
            | ||||| |||| ||| |||| |||| |             | |  | |||||  || ||| ||| |||||| ||   
............G.EQRTT.QGQV.FLH.QTGV.TWHD.R.............G.L..G.EIRNT..GR.YFV.HNN.TTQFTD.RL   
----250-------260-------270-------280-------290-------300-------310-------320-------330

Entity_assembly_ID: B, Chain length: 20, Sequence coverage: 15.0%

Total number of restraints: 49
Potential type of restraints: undefined (49)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords modular binding, PY motif, Smurf2, TGF-beta, WW