BMRBj - BMREntryMaster

Found 1 Document (2.062 seconds)

BMRB: 30969

Solution Structure of Sds3 Capped Tudor Domain

Authors

Marcum, R.D., Radhakrishnan, I.

Assembly

Sin3 histone deacetylase corepressor complex component SDS3

Entity

1. Sin3 histone deacetylase corepressor complex component SDS3 (polymer), 79 monomers, 9373.573 Da Detail

SNAQRFEARI EDGKLYYDKR WYHKSQAIYL ESKDNQKLSC VISSVGANEI WVRKTSDSTK MRIYVGQLQR GLFVIRRRS

Formula weight

9373.573 Da

Source organism

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.3 %, Completeness (bb): 98.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.3 % (897 of 982)	89.3 % (459 of 514)	94.3 % (349 of 370)	90.8 % (89 of 98)
Backbone	98.3 % (466 of 474)	98.8 % (160 of 162)	98.3 % (229 of 233)	97.5 % (77 of 79)
Sidechain	86.8 % (506 of 583)	84.9 % (299 of 352)	92.0 % (195 of 212)	63.2 % (12 of 19)
Aromatic	61.4 % (54 of 88)	61.4 % (27 of 44)	59.5 % (25 of 42)	100.0 % (2 of 2)
Methyl	100.0 % (76 of 76)	100.0 % (38 of 38)	100.0 % (38 of 38)

1. entity 1

SNAQRFEARI EDGKLYYDKR WYHKSQAIYL ESKDNQKLSC VISSVGANEI WVRKTSDSTK MRIYVGQLQR GLFVIRRRS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.35 mM [U-100% 15N] Sds3 CTD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Sds3 CTD	[U-100% 15N]		0.35 mM
2	sodium phosphate buffer	natural abundance		20 mM
3	NaCl	natural abundance		50 mM
4	DTT	natural abundance		1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.35 mM [U-100% 13C; U-100% 15N] Sds3 CTD, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	Sds3 CTD	[U-100% 13C; U-100% 15N]		0.35 mM
6	sodium phosphate buffer	natural abundance		20 mM
7	NaCl	natural abundance		50 mM
8	DTT	natural abundance		1 mM

Release date

2021-11-29

Citation

A capped Tudor domain within a core subunit of the Sin3L/Rpd3L histone deacetylase complex binds to nucleic acid G-quadruplexes
Marcum, R.D., Hsieh, J., Giljen, M., Justice, E., Daffern, N., Zhang, Y., Radhakrishnan, I.
J. Biol. Chem. (2022), 298, 101558-101558, PubMed 34979096 , DOI 10.1016/j.jbc.2021.101558 , Abstract

Related entities 1. Sin3 histone deacetylase corepressor complex component SDS3, : 2 : 19 entities Detail

Interaction partners 1. Sin3 histone deacetylase corepressor complex component SDS3, : 5 interactors Detail

More details for 5 interactors identified by 2 citations

Experiments performed 8 experiments Detail

1 3D 1H-15N NOESY

Instrument

Agilent Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.35 mM [U-100% 15N] Sds3 CTD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Sds3 CTD	[U-100% 15N]		0.35 mM
2	sodium phosphate buffer	natural abundance		20 mM
3	NaCl	natural abundance		50 mM
4	DTT	natural abundance		1 mM

2 3D 1H-13C NOESY aliphatic

Instrument

Agilent Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.35 mM [U-100% 13C; U-100% 15N] Sds3 CTD, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	Sds3 CTD	[U-100% 13C; U-100% 15N]		0.35 mM
6	sodium phosphate buffer	natural abundance		20 mM
7	NaCl	natural abundance		50 mM
8	DTT	natural abundance		1 mM

3 2D 1H-1H NOESY

Instrument

Agilent Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.35 mM [U-100% 13C; U-100% 15N] Sds3 CTD, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	Sds3 CTD	[U-100% 13C; U-100% 15N]		0.35 mM
6	sodium phosphate buffer	natural abundance		20 mM
7	NaCl	natural abundance		50 mM
8	DTT	natural abundance		1 mM

4 3D CBCA(CO)NH

Instrument

Agilent Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.35 mM [U-100% 13C; U-100% 15N] Sds3 CTD, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	Sds3 CTD	[U-100% 13C; U-100% 15N]		0.35 mM
6	sodium phosphate buffer	natural abundance		20 mM
7	NaCl	natural abundance		50 mM
8	DTT	natural abundance		1 mM

5 3D HNCACB

Instrument

Agilent Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.35 mM [U-100% 13C; U-100% 15N] Sds3 CTD, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	Sds3 CTD	[U-100% 13C; U-100% 15N]		0.35 mM
6	sodium phosphate buffer	natural abundance		20 mM
7	NaCl	natural abundance		50 mM
8	DTT	natural abundance		1 mM

6 3D C(CO)NH

Instrument

Agilent Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.35 mM [U-100% 13C; U-100% 15N] Sds3 CTD, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	Sds3 CTD	[U-100% 13C; U-100% 15N]		0.35 mM
6	sodium phosphate buffer	natural abundance		20 mM
7	NaCl	natural abundance		50 mM
8	DTT	natural abundance		1 mM

7 3D HCCH-TOCSY

Instrument

Agilent Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.35 mM [U-100% 13C; U-100% 15N] Sds3 CTD, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	Sds3 CTD	[U-100% 13C; U-100% 15N]		0.35 mM
6	sodium phosphate buffer	natural abundance		20 mM
7	NaCl	natural abundance		50 mM
8	DTT	natural abundance		1 mM

8 3D HCCH-COSY

Instrument

Agilent Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.35 mM [U-100% 13C; U-100% 15N] Sds3 CTD, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	Sds3 CTD	[U-100% 13C; U-100% 15N]		0.35 mM
6	sodium phosphate buffer	natural abundance		20 mM
7	NaCl	natural abundance		50 mM
8	DTT	natural abundance		1 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30969_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: bmr30969_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	972		100.0 (chain: 1, length: 79)
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: 79, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 534
  - ¹³C chemical shifts: 349
  - ¹⁵N chemical shifts: 89
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- 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: 1

Keywords G-quadruplex binding, GENE REGULATION, Nucleic acid binding, Transcriptional corepressor, Tudor domain