BMRB Entry 34692

Name: NMR structure of Npl3 RRM12 bound to the AUCCAGUGGAA RNA
Published: 2022-12-16

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PDB ID: 7qde
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34692
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR structure of Npl3 RRM12 bound to the AUCCAGUGGAA RNA PubMed: 37935663

Deposition date: 2021-11-26 Original release date: 2022-12-16

Authors: Allain, F.; Clery, A.; Moursy, A.

Citation: Moursy, Ahmed; Clery, Antoine; Gerhardy, Stefan; Betz, Katharina; Rao, Sanjana; Mazur, Jaroslaw; Campagne, Sebastien; Beusch, Irene; Duszczyk, Malgorzata; Robinson, Mark; Panse, Vikram Govind; Allain, Frederic H-T. "RNA recognition by Npl3p reveals U2 snRNA-binding compatible with a chaperone role during splicing" Nat. Commun. 14, 7166-7166 (2023).

Assembly members:
entity_1, polymer, 11 residues, 3530.178 Da.
entity_2, polymer, 169 residues, 19294.615 Da.

Natural source: Common Name: Baker's yeast Taxonomy ID: 559292 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source: Production method: recombinant technology Host organism: unidentified plasmid

Entity Sequences (FASTA):
entity_1: AUCCAGUGGAA
entity_2: MHHRQEGELSNTRLFVRPFP LDVQESELNEIFGPFGPMKE VKILNGFAFVEFEEAESAAK AIEEVHGKSFANQPLEVVYS KLPAKRYRITMKNLPEGCSW QDLKDLARENSLETTFSSVN TRDFDGTGALEFPSEEILVE ALERLNNIEFRGSVITVERD DNPPPIRRS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	356
15N chemical shifts	146
1H chemical shifts	618

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 11 residues - 3530.178 Da.

1

A

U

C

A

G

U

G

A

2

A

Entity 2, unit_2 169 residues - 19294.615 Da.

1

MET

HIS

ARG

GLN

GLU

GLY

GLU

LEU

SER

2

ASN

THR

ARG

LEU

PHE

VAL

ARG

PRO

PHE

PRO

3

LEU

ASP

VAL

GLN

GLU

SER

GLU

LEU

ASN

GLU

4

ILE

PHE

GLY

PRO

PHE

GLY

PRO

MET

LYS

GLU

5

VAL

LYS

ILE

LEU

ASN

GLY

PHE

ALA

PHE

VAL

6

GLU

PHE

GLU

ALA

GLU

SER

ALA

LYS

7

ALA

ILE

GLU

VAL

HIS

GLY

LYS

SER

PHE

8

ALA

ASN

GLN

PRO

LEU

GLU

VAL

TYR

SER

9

LYS

LEU

PRO

ALA

LYS

ARG

TYR

ARG

ILE

THR

10

MET

LYS

ASN

LEU

PRO

GLU

GLY

CYS

SER

TRP

11

GLN

ASP

LEU

LYS

ASP

LEU

ALA

ARG

GLU

ASN

12

SER

LEU

GLU

THR

PHE

SER

VAL

ASN

13

THR

ARG

ASP

PHE

ASP

GLY

THR

GLY

ALA

LEU

14

GLU

PHE

PRO

SER

GLU

ILE

LEU

VAL

GLU

15

ALA

LEU

GLU

ARG

LEU

ASN

ILE

GLU

PHE

16

ARG

GLY

SER

VAL

ILE

THR

VAL

GLU

ARG

ASP

17

ASP

ASN

PRO

ILE

ARG

SER

Samples:

sample_1: Npl3 RRM12, [U-15N], 0.9 mM

sample_2: Npl3 RRM12, [U-100% 13C; U-100% 15N], 0.9 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.9; pressure: 0 Pa; temperature: 313 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
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1
2D NOESY F1F2f	sample_2	isotropic	sample_conditions_1
2D NOESY F2f	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1

Software:

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

CYANA, Guntert, Mumenthaler and Wuthrich - peak picking, structure calculation

Sparky, Goddard - chemical shift assignment

NMR spectrometers:

Bruker AVANCE 900 MHz
Bruker AVANCE III 700 MHz
Bruker AVANCE III 600 MHz

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