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BMRB: 30722

6VTI

Solution NMR structure of the N-terminal domain of the Serine/threonine-protein phosphatase 1 regulatory subunit 10, PPP1R10

Authors

Lemak, A., Wei, Y., Duan, S., Houliston, S., Penn, L.Z., Arrowsmith, C.H.

Assembly

E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27)

Entity

1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27) (polymer), 148 monomers, 16626.28 Da Detail

MGSGPIDPKE LLKGLDSFLT RDGEVKSVDG IAKIFSLMKE ARKMVSRCTY LNIILQTRAP EVLVKFIDVG GYKLLNSWLT YSKTTNNIPL LQQILLTLQH LPLTVDHLKQ NNTAKLVKQL SKSSEDEELR KLASVLVSDW MAVIRSQS

Formula weight

16626.28 Da

Source organism

Rattus norvegicus

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.4 %, Completeness (bb): 96.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.4 % (1644 of 1779)	92.2 % (855 of 927)	91.5 % (635 of 694)	97.5 % (154 of 158)
Backbone	96.5 % (847 of 878)	96.3 % (287 of 298)	96.1 % (420 of 437)	97.9 % (140 of 143)
Sidechain	89.7 % (935 of 1042)	90.3 % (568 of 629)	88.7 % (353 of 398)	93.3 % (14 of 15)
Aromatic	64.0 % (55 of 86)	74.4 % (32 of 43)	51.2 % (21 of 41)	100.0 % (2 of 2)
Methyl	99.0 % (204 of 206)	99.0 % (102 of 103)	99.0 % (102 of 103)

1. entity 1

MGSGPIDPKE LLKGLDSFLT RDGEVKSVDG IAKIFSLMKE ARKMVSRCTY LNIILQTRAP EVLVKFIDVG GYKLLNSWLT YSKTTNNIPL LQQILLTLQH LPLTVDHLKQ NNTAKLVKQL SKSSEDEELR KLASVLVSDW MAVIRSQS

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details 450 uM [U-13C; U-15N] PPP1R10 N-terminal domain, 2.5 % glycerol, 200 mM NaCl, 20 mM HEPES, 1 mM DTT, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PPP1R10 N-terminal domain	[U-13C; U-15N]	450 (±50.0) uM
2	glycerol	natural abundance	2.5 %
3	NaCl	natural abundance	200 mM
4	HEPES	natural abundance	20 mM
5	DTT	natural abundance	1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6VTI, Strand ID: A Detail

Release date

2020-02-19

Citation

The MYC oncoprotein directly interacts with its chromatin cofactor PNUTS to recruit PP1 phosphatase
Wei, Y., Redel, C., Ahlner, A., Lemak, A., Johansson-Akhe, I., Houliston, S., Kenney, T., Tamachi, A., Morad, V., Duan, S., Andrews, D.W., Wallner, B., Sunnerhagen, M., Arrowsmith, C.H., Penn, L.Z.
Nucleic Acids Res. (2022), 50, 3505-3522, PubMed 35244724 , DOI 10.1093/nar/gkac138 , Abstract

Related entities 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), : 1 : 3 : 2 : 18 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), : 8 interactors Detail

More details for 8 interactors identified by 3 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE II - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details 450 uM [U-13C; U-15N] PPP1R10 N-terminal domain, 2.5 % glycerol, 200 mM NaCl, 20 mM HEPES, 1 mM DTT, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PPP1R10 N-terminal domain	[U-13C; U-15N]	450 (±50.0) uM
2	glycerol	natural abundance	2.5 %
3	NaCl	natural abundance	200 mM
4	HEPES	natural abundance	20 mM
5	DTT	natural abundance	1 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PPP1R10 N-terminal domain	[U-13C; U-15N]	450 (±50.0) uM
2	glycerol	natural abundance	2.5 %
3	NaCl	natural abundance	200 mM
4	HEPES	natural abundance	20 mM
5	DTT	natural abundance	1 mM

3 3D HN(CO)CA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PPP1R10 N-terminal domain	[U-13C; U-15N]	450 (±50.0) uM
2	glycerol	natural abundance	2.5 %
3	NaCl	natural abundance	200 mM
4	HEPES	natural abundance	20 mM
5	DTT	natural abundance	1 mM

4 3D HNCA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PPP1R10 N-terminal domain	[U-13C; U-15N]	450 (±50.0) uM
2	glycerol	natural abundance	2.5 %
3	NaCl	natural abundance	200 mM
4	HEPES	natural abundance	20 mM
5	DTT	natural abundance	1 mM

5 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PPP1R10 N-terminal domain	[U-13C; U-15N]	450 (±50.0) uM
2	glycerol	natural abundance	2.5 %
3	NaCl	natural abundance	200 mM
4	HEPES	natural abundance	20 mM
5	DTT	natural abundance	1 mM

6 3D HBHA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PPP1R10 N-terminal domain	[U-13C; U-15N]	450 (±50.0) uM
2	glycerol	natural abundance	2.5 %
3	NaCl	natural abundance	200 mM
4	HEPES	natural abundance	20 mM
5	DTT	natural abundance	1 mM

7 3D 1H-15N NOESY

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PPP1R10 N-terminal domain	[U-13C; U-15N]	450 (±50.0) uM
2	glycerol	natural abundance	2.5 %
3	NaCl	natural abundance	200 mM
4	HEPES	natural abundance	20 mM
5	DTT	natural abundance	1 mM

8 3D HNCO

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PPP1R10 N-terminal domain	[U-13C; U-15N]	450 (±50.0) uM
2	glycerol	natural abundance	2.5 %
3	NaCl	natural abundance	200 mM
4	HEPES	natural abundance	20 mM
5	DTT	natural abundance	1 mM

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PPP1R10 N-terminal domain	[U-13C; U-15N]	450 (±50.0) uM
2	glycerol	natural abundance	2.5 %
3	NaCl	natural abundance	200 mM
4	HEPES	natural abundance	20 mM
5	DTT	natural abundance	1 mM

10 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PPP1R10 N-terminal domain	[U-13C; U-15N]	450 (±50.0) uM
2	glycerol	natural abundance	2.5 %
3	NaCl	natural abundance	200 mM
4	HEPES	natural abundance	20 mM
5	DTT	natural abundance	1 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30722_3.str
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

Content subtype: bmr30722_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1852		100.0 (chain: 1, length: 148)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 148, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 1070
  - ¹³C chemical shifts: 629
  - ¹⁵N chemical shifts: 153
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	927	860	92.8
¹³C chemical shifts	694	629	90.6
¹⁵N chemical shifts	164	153	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	298	293	98.3
¹³C chemical shifts	296	285	96.3
¹⁵N chemical shifts	143	139	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	629	567	90.1
¹³C chemical shifts	398	344	86.4
¹⁵N chemical shifts	21	14	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	105	98.1
¹³C chemical shifts	107	105	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	32	74.4
¹³C chemical shifts	41	20	48.8
¹⁵N chemical shifts	2	2	100.0

Keywords NUCLEAR PROTEIN, PP1-PNUTS phosphatase complex, Regulatory Subunit, c-MYC oncoprotein

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Found 1 Document (2.983 seconds)

BMRB: 30722

Sample

Related entities 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), : 1 : 3 : 2 : 18 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), : 8 interactors Detail

Experiments performed 10 experiments Detail

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Chemical shift validation 3 contents Detail