BMRBj - BMREntryMaster

Found 1 Document (0.933 seconds)

BMRB: 30197

5TR5

Solution structure of Serine 65 phosphorylated UBL domain from parkin

Authors

Aguirre, J.D., Dunkerley, K.M., Mercier, P., Shaw, G.S.

Assembly

E3 ubiquitin-protein ligase parkin (E.C.6.3.2.-)

Entity

1. E3 ubiquitin-protein ligase parkin (E.C.6.3.2.-) (polymer, Thiol state: all free), 76 monomers, 8903.963 Da Detail

MIVFVRFNSS HGFPVEVDSD TSIFQLKEVV AKRQGVPADQ LRVIFAGKEL RNDWTVQNCD LDQQXIVHIV QRPWRK

Formula weight

8903.963 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.7 %, Completeness: 89.0 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.0 % (816 of 917)	85.4 % (409 of 479)	93.8 % (332 of 354)	89.3 % (75 of 84)
Backbone	97.1 % (431 of 444)	98.0 % (147 of 150)	96.4 % (214 of 222)	97.2 % (70 of 72)
Sidechain	83.9 % (457 of 545)	79.6 % (262 of 329)	93.1 % (190 of 204)	41.7 % (5 of 12)
Aromatic	70.7 % (58 of 82)	70.7 % (29 of 41)	69.2 % (27 of 39)	100.0 % (2 of 2)
Methyl	100.0 % (90 of 90)	100.0 % (45 of 45)	100.0 % (45 of 45)

1. E3 ubiquitin-protein ligase parkin

MIVFVRFNSS HGFPVEVDSD TSIFQLKEVV AKRQGVPADQ LRVIFAGKEL RNDWTVQNCD LDQQXIVHIV QRPWRK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM [U-15N] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	200 uM
2	HEPES	natural abundance	25 mM
3	TCEP	natural abundance	250 uM
4	imidazole	natural abundance	300 uM
5	pUBL	[U-15N]	300 uM
6	sodium chloride	natural abundance	100 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM [U-13C] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	DSS	natural abundance	200 uM
10	HEPES	natural abundance	25 mM
11	TCEP	natural abundance	250 uM
12	imidazole	natural abundance	300 uM
13	pUBL	[U-13C]	300 uM
14	sodium chloride	natural abundance	100 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 400 uM [U-99% 13C; U-99% 15N] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
17	DSS	natural abundance	200 uM
18	HEPES	natural abundance	25 mM
19	TCEP	natural abundance	250 uM
20	imidazole	natural abundance	300 uM
21	pUBL	[U-99% 13C; U-99% 15N]	400 uM
22	sodium chloride	natural abundance	100 mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 400 uM pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 100% D2O

#	Name	Isotope labeling	Concentration
25	DSS	natural abundance	200 uM
26	HEPES	natural abundance	25 mM
27	TCEP	natural abundance	250 uM
28	imidazole	natural abundance	300 uM
29	pUBL	natural abundance	400 uM
30	sodium chloride	natural abundance	100 mM
31	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 25 models in PDB: 5TR5, Strand ID: A Detail

Release date

2016-11-10

Citation

Structure of phosphorylated UBL domain and insights into PINK1-orchestrated parkin activation
Aguirre, J.D., Dunkerley, K.M., Mercier, P., Shaw, G.S.
Proc. Natl. Acad. Sci. U. S. A. (2017), 114, 298-303, PubMed 28007983 , DOI 10.1073/pnas.1613040114 , Abstract

Related entities 1. E3 ubiquitin-protein ligase parkin (E.C.6.3.2.-), : 1 : 1 : 8 : 602 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase parkin (E.C.6.3.2.-), : 39 interactors Detail

More details for 39 interactors identified by 21 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM [U-15N] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	200 uM
2	HEPES	natural abundance	25 mM
3	TCEP	natural abundance	250 uM
4	imidazole	natural abundance	300 uM
5	pUBL	[U-15N]	300 uM
6	sodium chloride	natural abundance	100 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM [U-13C] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	DSS	natural abundance	200 uM
10	HEPES	natural abundance	25 mM
11	TCEP	natural abundance	250 uM
12	imidazole	natural abundance	300 uM
13	pUBL	[U-13C]	300 uM
14	sodium chloride	natural abundance	100 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

3 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 400 uM pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 100% D2O

#	Name	Isotope labeling	Concentration
25	DSS	natural abundance	200 uM
26	HEPES	natural abundance	25 mM
27	TCEP	natural abundance	250 uM
28	imidazole	natural abundance	300 uM
29	pUBL	natural abundance	400 uM
30	sodium chloride	natural abundance	100 mM
31	D2O	natural abundance	100 %

4 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 400 uM [U-99% 13C; U-99% 15N] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
17	DSS	natural abundance	200 uM
18	HEPES	natural abundance	25 mM
19	TCEP	natural abundance	250 uM
20	imidazole	natural abundance	300 uM
21	pUBL	[U-99% 13C; U-99% 15N]	400 uM
22	sodium chloride	natural abundance	100 mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DSS	natural abundance	200 uM
18	HEPES	natural abundance	25 mM
19	TCEP	natural abundance	250 uM
20	imidazole	natural abundance	300 uM
21	pUBL	[U-99% 13C; U-99% 15N]	400 uM
22	sodium chloride	natural abundance	100 mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

6 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DSS	natural abundance	200 uM
18	HEPES	natural abundance	25 mM
19	TCEP	natural abundance	250 uM
20	imidazole	natural abundance	300 uM
21	pUBL	[U-99% 13C; U-99% 15N]	400 uM
22	sodium chloride	natural abundance	100 mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DSS	natural abundance	200 uM
18	HEPES	natural abundance	25 mM
19	TCEP	natural abundance	250 uM
20	imidazole	natural abundance	300 uM
21	pUBL	[U-99% 13C; U-99% 15N]	400 uM
22	sodium chloride	natural abundance	100 mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

8 2D (HB)CB(CGCD)HD

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
25	DSS	natural abundance	200 uM
26	HEPES	natural abundance	25 mM
27	TCEP	natural abundance	250 uM
28	imidazole	natural abundance	300 uM
29	pUBL	natural abundance	400 uM
30	sodium chloride	natural abundance	100 mM
31	D2O	natural abundance	100 %

9 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DSS	natural abundance	200 uM
18	HEPES	natural abundance	25 mM
19	TCEP	natural abundance	250 uM
20	imidazole	natural abundance	300 uM
21	pUBL	[U-99% 13C; U-99% 15N]	400 uM
22	sodium chloride	natural abundance	100 mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DSS	natural abundance	200 uM
18	HEPES	natural abundance	25 mM
19	TCEP	natural abundance	250 uM
20	imidazole	natural abundance	300 uM
21	pUBL	[U-99% 13C; U-99% 15N]	400 uM
22	sodium chloride	natural abundance	100 mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

11 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
9	DSS	natural abundance	200 uM
10	HEPES	natural abundance	25 mM
11	TCEP	natural abundance	250 uM
12	imidazole	natural abundance	300 uM
13	pUBL	[U-13C]	300 uM
14	sodium chloride	natural abundance	100 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

12 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
25	DSS	natural abundance	200 uM
26	HEPES	natural abundance	25 mM
27	TCEP	natural abundance	250 uM
28	imidazole	natural abundance	300 uM
29	pUBL	natural abundance	400 uM
30	sodium chloride	natural abundance	100 mM
31	D2O	natural abundance	100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30197_5tr5.nef
Input source #2: Coordindates	5tr5.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)
1:64:GLN:C	1:65:SEP:N	unknown	unknown	n/a
1:65:SEP:C	1:66:ILE:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	65	SEP	PHOSPHOSERINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70------
MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQXIVHIVQRPWRK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQXIVHIVQRPWRK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	76	0	0	100.0

Content subtype: combined_30197_5tr5.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_chemical_shifts_1	Warning	825		100.0 (chain: A, length: 76)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1477 (1)	noe	96.1 (chain: A, length: 76)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	37 (37)	.	35.5 (chain: A, length: 76)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 410
  - ¹³C chemical shifts: 335
  - ¹⁵N chemical shifts: 80
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
11	HIS	ND1	230.7335
11	HIS	NE2	179.056
65	SEP	C	173.4499
68	HIS	ND1	235.1261
68	HIS	NE2	176.4721

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	483	410	84.9
¹³C chemical shifts	356	334	93.8
¹⁵N chemical shifts	91	76	83.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	152	149	98.0
¹³C chemical shifts	151	143	94.7
¹⁵N chemical shifts	73	71	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	331	261	78.9
¹³C chemical shifts	205	191	93.2
¹⁵N chemical shifts	18	5	27.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	46	100.0
¹³C chemical shifts	46	46	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	29	70.7
¹³C chemical shifts	39	27	69.2
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 96.1%
- Total number of restraints: 1477
- Weight of restraints: 1.0 (1477)
- Potential type of restraints: square-well-parabolic (1477)
- Range of distance target values: 1.29, 2.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 35.5%
- Total number of restraints: 37
- Total number of restraints per polymer type: 37
- Weight of restraints: 1.0 (37)
- Potential type of restraints: square-well-parabolic (37)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords PINK1, Parkinson's disease, phosphorylation

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Found 1 Document (0.933 seconds)

BMRB: 30197

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. E3 ubiquitin-protein ligase parkin (E.C.6.3.2.-), : 1 : 1 : 8 : 602 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase parkin (E.C.6.3.2.-), : 39 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 4 contents Detail