BMRB Entry 34691

Name: NMR structure of Npl3 RRM1 bound to the AUCCAA RNA
Published: 2022-10-21

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PDB ID: 7qdd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34691
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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: NMR structure of Npl3 RRM1 bound to the AUCCAA RNA PubMed: 37935663

Deposition date: 2021-11-26 Original release date: 2022-10-21

Authors: Clery, A.; Allain, F.; 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, 6 residues, 1859.189 Da.
entity_2, polymer, 88 residues, 10121.476 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: AUCCAA
entity_2: MHHRQEGELSNTRLFVRPFP LDVQESELNEIFGPFGPMKE VKILNGFAFVEFEEAESAAK AIEEVHGKSFANQPLEVVYS KLPAKRYR

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	266
15N chemical shifts	80
1H chemical shifts	624

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 6 residues - 1859.189 Da.

1

A

U

C

A

Entity 2, unit_2 88 residues - 10121.476 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

Samples:

sample_1: Npl3 RRM1, [U-15N], 0.9 mM

sample_2: Npl3 RRM1, [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 F1fF2f	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 HD 700 MHz
Bruker AVANCE III HD 600 MHz

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