BMRB Entry 36310

Name: SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH DOMAIN-2 CONTAINING PROTEIN 2
Published: 2025-10-11

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36310

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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 THE YTH DOMAIN IN YTH DOMAIN-2 CONTAINING PROTEIN 2

Deposition date:

2020-01-15

Original release date:

2025-10-11

Authors:

Muto, Y.; Kobayashi, N.; Yokoyama, S.; RIKEN Structural Genomics/Proteomics Initiative (RSGI), .

Citation:

Citation: Endo, R.; He, F.; Inoue, M.; Muto, Y.; Kigawa, T.; Shirouzu, M.; Yokoyama, S.. "SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH DOMAIN-CONTAINING PROTEIN 2" .

Assembly members:

Assembly members:
YTH domain containing protein 2 (YTHDC2), polymer, 141 residues, 16138.065 Da.

Natural source:

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Cell-free gateway cloning vector N-term 8xHis eGFP pCellFree_G03 Vector: P060508-16

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YTH domain containing protein 2 (YTHDC2): GSSGSSGVRYFIMKSSNLRN LEISQQKGIWSTTPSNERKL NRAFWESSIVYLVFSVQGSG HFQGFSRMSSEIGREKSQDW GSAGLGGVFKVEWIRKESLP FQFAHHLLNPWNDNKKVQIS RDGQELEPQVGEQLLQLWER L

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	615
15N chemical shifts	147
1H chemical shifts	990

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 141 residues - 16138.065 Da.

1

GLY

SER

GLY

SER

GLY

VAL

ARG

TYR

2

PHE

ILE

MET

LYS

SER

ASN

LEU

ARG

ASN

3

LEU

GLU

ILE

SER

GLN

LYS

GLY

ILE

TRP

4

SER

THR

PRO

SER

ASN

GLU

ARG

LYS

LEU

5

ASN

ARG

ALA

PHE

TRP

GLU

SER

ILE

VAL

6

TYR

LEU

VAL

PHE

SER

VAL

GLN

GLY

SER

GLY

7

HIS

PHE

GLN

GLY

PHE

SER

ARG

MET

SER

8

GLU

ILE

GLY

ARG

GLU

LYS

SER

GLN

ASP

TRP

9

GLY

SER

ALA

GLY

LEU

GLY

VAL

PHE

LYS

10

VAL

GLU

TRP

ILE

ARG

LYS

GLU

SER

LEU

PRO

11

PHE

GLN

PHE

ALA

HIS

LEU

ASN

PRO

12

TRP

ASN

ASP

ASN

LYS

VAL

GLN

ILE

SER

13

ARG

ASP

GLY

GLN

GLU

LEU

GLU

PRO

GLN

VAL

14

GLY

GLU

GLN

LEU

GLN

LEU

TRP

GLU

ARG

15

LEU

Samples:

sample_1: helicase, [U-99% 13C; U-99% 15N], 1.0 mg/mL; NaN3 0.02%; dithiothreitol 1 mM; NaCl 100 mM; Tris-HCl 20 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D_13C,15N-SEPARATED_NOESY SPECTRA	sample_1	isotropic	sample_conditions_1

Software:

Amber v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v2.0.17, Guntert, Mumenthaler and Wuthrich - structure calculation

KUJIRA v0.9820, N. Kobayashi, T. Kigawa, S. Yokoyama - chemical shift assignment

NMRView v5.0.4, Johnson, One Moon Scientific - peak picking

NMR spectrometers:

Bruker AVANCE 800 MHz

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