BMRB Entry 30969

Name: Solution Structure of Sds3 Capped Tudor Domain
Published: 2022-01-14

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PDB ID: 7sxi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30969
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of Sds3 Capped Tudor Domain

Deposition date:

2021-11-23

Original release date:

2022-01-14

Authors:

Marcum, R.; Radhakrishnan, I.

Citation:

Citation: Marcum, R.; Hsieh, J.; Giljen, M.; Justice, E.; Daffern, N.; Zhang, Y.; Radhakrishnan, I.. "A Capped Tudor Domain within a Core Subunit of the Sin3L/Rpd3L Histone Deacetylase Complex Binds to Nucleic Acid G-Quadruplexes" J. Biol. Chem. 298, 101558-101558 (2021).
PubMed: 34979096

Assembly members:

Assembly members:
entity_1, polymer, 79 residues, 9390.714 Da.

Natural source:

Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SNAQRFEARIEDGKLYYDKR WYHKSQAIYLESKDNQKLSC VISSVGANEIWVRKTSDSTK MRIYVGQLQRGLFVIRRRS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	349
15N chemical shifts	89
1H chemical shifts	534

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 79 residues - 9390.714 Da.

1

SER

ASN

ALA

GLN

ARG

PHE

GLU

ALA

ARG

ILE

2

GLU

ASP

GLY

LYS

LEU

TYR

ASP

LYS

ARG

3

TRP

TYR

HIS

LYS

SER

GLN

ALA

ILE

TYR

LEU

4

GLU

SER

LYS

ASP

ASN

GLN

LYS

LEU

SER

CYS

5

VAL

ILE

SER

VAL

GLY

ALA

ASN

GLU

ILE

6

TRP

VAL

ARG

LYS

THR

SER

ASP

SER

THR

LYS

7

MET

ARG

ILE

TYR

VAL

GLY

GLN

LEU

GLN

ARG

8

GLY

LEU

PHE

VAL

ILE

ARG

SER

Samples:

sample_1: Sds3 CTD, [U-100% 15N], 0.35 mM; sodium phosphate buffer 20 mM; NaCl 50 mM; DTT 1 mM

sample_2: Sds3 CTD, [U-100% 13C; U-100% 15N], 0.35 mM; sodium phosphate buffer 20 mM; NaCl 50 mM; DTT 1 mM

sample_conditions_1: ionic strength: 0.07 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1

Software:

Felix, Accelrys Software Inc. - processing

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure calculation

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL. Bioinformatics. 2015 Apr 15; 31(8):1325-7. - chemical shift assignment, peak picking

NMR spectrometers:

Agilent Direct Drive 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks