Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR26587

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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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Name: Backbone chemical shifts of Roquin ROQ domain in complex with Ox40 stem-hexa-loop RNA
Published: 2016-10-04

Title:

Backbone chemical shifts of Roquin ROQ domain in complex with Ox40 stem-hexa-loop RNA

Deposition date:

2015-06-16

Original release date:

2016-10-04

Authors:

Schlundt, Andreas; Sattler, Michael

Citation:

Citation: Janowski, Robert; Heinz, Gitta; Schlundt, Andreas; Wommelsdorf, Nina; Brenner, Sven; Gruber, Andreas; Blank, Michael; Buch, Thorsten; Buhmann, Raymund; Zavolan, Mihaela; Niessing, Dierk; Heissmeyer, Vigo; Sattler, Michael. "Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40" Nat. Comm. 7, 11032-11032 (2016).
PubMed: 27010430

Assembly members:

Assembly members:
Roquin_ROQ_domain, polymer, 151 residues, 17773.4 Da.
Ox40 hexa-loop RNA, polymer, 22 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pETTrx1a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Roquin_ROQ_domain: PQQLSSNLWAAVRARGCQFL GPAMQEEALKLVLLALEDGS ALSRKVLVLFVVQRLEPRFP QASKTSIGHVVQLLYRASCF KVTKRDEDSSLMQLKEEFRT YEALRREHDSQIVQIAMEAG LRIAPDQWSSLLYGDQSHKS HMQSIIDKLQT
Ox40 hexa-loop RNA: UCCACACCGUUCUAGGUGCU GG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	296
15N chemical shifts	144
1H chemical shifts	144

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ROQ domain	1
2	Ox40 hexa-loop RNA	2

Entities:

Entity 1, ROQ domain 151 residues - 17773.4 Da.

Construct was from 171-326 but sequential assignments only available from 176-326.

1

PRO

GLN

LEU

SER

ASN

LEU

TRP

ALA

2

ALA

VAL

ARG

ALA

ARG

GLY

CYS

GLN

PHE

LEU

3

GLY

PRO

ALA

MET

GLN

GLU

ALA

LEU

LYS

4

LEU

VAL

LEU

ALA

LEU

GLU

ASP

GLY

SER

5

ALA

LEU

SER

ARG

LYS

VAL

LEU

VAL

LEU

PHE

6

VAL

GLN

ARG

LEU

GLU

PRO

ARG

PHE

PRO

7

GLN

ALA

SER

LYS

THR

SER

ILE

GLY

HIS

VAL

8

VAL

GLN

LEU

TYR

ARG

ALA

SER

CYS

PHE

9

LYS

VAL

THR

LYS

ARG

ASP

GLU

ASP

SER

10

LEU

MET

GLN

LEU

LYS

GLU

PHE

ARG

THR

11

TYR

GLU

ALA

LEU

ARG

GLU

HIS

ASP

SER

12

GLN

ILE

VAL

GLN

ILE

ALA

MET

GLU

ALA

GLY

13

LEU

ARG

ILE

ALA

PRO

ASP

GLN

TRP

SER

14

LEU

TYR

GLY

ASP

GLN

SER

HIS

LYS

SER

15

HIS

MET

GLN

SER

ILE

ASP

LYS

LEU

GLN

16

THR

Entity 2, Ox40 hexa-loop RNA

Samples:

sample_1: Roquin ROQ domain, [U-99% 13C; U-99% 15N], 0.4 mM; Ox40 hexa-loop RNA 0.46 mM; D2O, [U-100% 2H], 10%; TRIS 20 mM; sodium chloride 150 mM; TCEP 4 mM; sodium azide 0.02%; H2O, [U-100% 2H], 90%

sample_conditions_1: ionic strength: 0.15 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1

Software:

CCPNMR_Analysis v2.4.0, CCPN - chemical shift assignment

NMR spectrometers:

Bruker Avance 600 MHz
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

BMRB Entry 26587