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BMRB: 16156

2KES

Solution Structure of the Coiled-coil Domain of Synphilin-1

Authors

Xie, Y., Zhou, C., Zhou, Z., Hu, H.

Assembly

Synphilin-1

Entity

1. Synphilin-1 (polymer, Thiol state: all free), 48 monomers, 5365.093 Da Detail

GSVETCMSLA SQVVKLTKQL KEQTVERVTL QNQLQQFLEA QKSEGKSL

Formula weight

5365.093 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.8 %, Completeness: 78.0 %, Completeness (bb): 94.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.0 % (446 of 572)	74.8 % (225 of 301)	81.3 % (174 of 214)	82.5 % (47 of 57)
Backbone	94.8 % (273 of 288)	94.9 % (93 of 98)	94.4 % (134 of 142)	95.8 % (46 of 48)
Sidechain	65.5 % (216 of 330)	65.0 % (132 of 203)	70.3 % (83 of 118)	11.1 % (1 of 9)
Aromatic	20.0 % (2 of 10)	40.0 % (2 of 5)	0.0 % (0 of 5)
Methyl	71.7 % (43 of 60)	80.0 % (24 of 30)	63.3 % (19 of 30)

1. Synphilin-1

GSVETCMSLA SQVVKLTKQL KEQTVERVTL QNQLQQFLEA QKSEGKSL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		0.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	natural abundance		10 %
5	H2O	natural abundance		90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		50 mM
9	D2O	natural abundance		10 %
10	H2O	natural abundance		90 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	entity	[U-13C; U-15N]		1 mM
12	sodium phosphate	natural abundance		20 mM
13	sodium chloride	natural abundance		50 mM
14	D2O	natural abundance		10 %
15	H2O	natural abundance		90 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2KES, Strand ID: A Detail

Release date

2009-03-08

Citation

Interaction with synphilin-1 promotes inclusion formation of alpha-synuclein: mechanistic insights and pathological implication
Xie, Y., Zhou, C., Zhou, Z., Hong, J., Lin, D., Hu, H.
FASEB J. (2010), 24, 196-205, PubMed 19762560 , DOI 10.1096/fj.09-133082 , Abstract

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

  BMRB: 15095 released on 2009-09-28
    Title Solution Structure of a Dodecapeptide from Alpha-Synuclein Bound with Synphilin-1
  Swiss-Prot: Q9Y6H5 released on 2000-12-01
    Title SNCAP_HUMAN Entity Synphilin-1

Related entities 1. Synphilin-1, : 1 : 2 : 11 entities Detail

Interaction partners 1. Synphilin-1, : 15 interactors Detail

More details for 15 interactors identified by 7 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		0.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	natural abundance		10 %
5	H2O	natural abundance		90 %

2 3D HNHA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		50 mM
9	D2O	natural abundance		10 %
10	H2O	natural abundance		90 %

3 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		50 mM
9	D2O	natural abundance		10 %
10	H2O	natural abundance		90 %

4 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	entity	[U-13C; U-15N]		1 mM
12	sodium phosphate	natural abundance		20 mM
13	sodium chloride	natural abundance		50 mM
14	D2O	natural abundance		10 %
15	H2O	natural abundance		90 %

5 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	entity	[U-13C; U-15N]		1 mM
12	sodium phosphate	natural abundance		20 mM
13	sodium chloride	natural abundance		50 mM
14	D2O	natural abundance		10 %
15	H2O	natural abundance		90 %

6 3D HBHA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	entity	[U-13C; U-15N]		1 mM
12	sodium phosphate	natural abundance		20 mM
13	sodium chloride	natural abundance		50 mM
14	D2O	natural abundance		10 %
15	H2O	natural abundance		90 %

7 3D HNCO

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	entity	[U-13C; U-15N]		1 mM
12	sodium phosphate	natural abundance		20 mM
13	sodium chloride	natural abundance		50 mM
14	D2O	natural abundance		10 %
15	H2O	natural abundance		90 %

8 3D HCCH-TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	entity	[U-13C; U-15N]		1 mM
12	sodium phosphate	natural abundance		20 mM
13	sodium chloride	natural abundance		50 mM
14	D2O	natural abundance		10 %
15	H2O	natural abundance		90 %

9 3D 1H-13C NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	entity	[U-13C; U-15N]		1 mM
12	sodium phosphate	natural abundance		20 mM
13	sodium chloride	natural abundance		50 mM
14	D2O	natural abundance		10 %
15	H2O	natural abundance		90 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16156_2kes.nef
Input source #2: Coordindates	2kes.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

510-----520-------530-------540-------550-------
GSVETCMSLASQVVKLTKQLKEQTVERVTLQNQLQQFLEAQKSEGKSL
||||||||||||||||||||||||||||||||||||||||||||||||
GSVETCMSLASQVVKLTKQLKEQTVERVTLQNQLQQFLEAQKSEGKSL
--------10--------20--------30--------40--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	48	0	0	100.0

Content subtype: combined_16156_2kes.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	443		95.8 (chain: A, length: 48)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	565 (1)	noe	93.8 (chain: A, length: 48)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 48, Sequence coverage: 95.8%
- Total number of assignments
  - ¹H chemical shifts: 223
  - ¹³C chemical shifts: 174
  - ¹⁵N chemical shifts: 46
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 48, Sequence coverage: 93.8%
- Total number of restraints: 565
- Weight of restraints: 1.0 (565)
- Potential type of restraints: square-well-parabolic (565)
- Range of distance target values: 1.49, 8.47 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords coiled-coil, Synphillin