BMRB Entry 34715

Name: Solution structure of RBM39 RRM1 bound to U1 snRNA stem loop 3
Published: 2023-03-23

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PDB ID: 7zap
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34715
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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 RBM39 RRM1 bound to U1 snRNA stem loop 3

Deposition date:

2022-03-22

Original release date:

2023-03-23

Authors:

Campagne, S.; Allain, F.

Citation:

Citation: Campagne, Sebastien; Jutzi, Daniel; Malard, Florian; Matoga, Maja; Romane, Ksenija; Feldmuller, Miki; Colombo, Martino; Ruepp, Marc-David; Allain, Frederic H-T. "Molecular basis of RNA-binding and autoregulation by the cancer-associated splicing factor RBM39" Nat. Commun. 14, 5366-5366 (2023).
PubMed: 37666821

Assembly members:

Assembly members:
entity_1, polymer, 97 residues, 10820.457 Da.
entity_2, polymer, 28 residues, 8954.375 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: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MIDNLTPEERDARTVFCMQL AARIRPRDLEEFFSTVGKVR DVRMISDRNSRRSKGIAYVE FVDVSSVPLAIGLTGQRVLG VPIIVQASQAEKNRAAA
entity_2: GGGAUUUCCCCAAAUGUGGG AAACUCCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	539
15N chemical shifts	1
1H chemical shifts	708

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 97 residues - 10820.457 Da.

1

MET

ILE

ASP

ASN

LEU

THR

PRO

GLU

ARG

2

ASP

ALA

ARG

THR

VAL

PHE

CYS

MET

GLN

LEU

3

ALA

ARG

ILE

ARG

PRO

ARG

ASP

LEU

GLU

4

GLU

PHE

SER

THR

VAL

GLY

LYS

VAL

ARG

5

ASP

VAL

ARG

MET

ILE

SER

ASP

ARG

ASN

SER

6

ARG

SER

LYS

GLY

ILE

ALA

TYR

VAL

GLU

7

PHE

VAL

ASP

VAL

SER

VAL

PRO

LEU

ALA

8

ILE

GLY

LEU

THR

GLY

GLN

ARG

VAL

LEU

GLY

9

VAL

PRO

ILE

VAL

GLN

ALA

SER

GLN

ALA

10

GLU

LYS

ASN

ARG

ALA

Entity 2, unit_2 28 residues - 8954.375 Da.

1

G

A

U

C

2

C

A

U

G

U

G

3

A

C

U

C

Samples:

sample_1: sodium phosphate 10 mM; DTT 3 mM; RBM39 RRM1, [U-13C; U-15N], 1.2 mM; U1 snRNA SL3 1.5 mM

sample_2: sodium phosphate 10 mM; DTT 3 mM; RBM39 RRM1, [U-13C; U-15N], 1.2 mM; U1 snRNA SL3 1.5 mM

sample_3: sodium phosphate 10 mM; DTT 3 mM; RBM39 RRM1, [U-13C; U-15N], 1.2 mM; U1 snRNA SL3 1.5 mM

sample_conditions_1: ionic strength: 10 mM; pH: 5.5; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D edited filtered 1H-13C NOESY HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H F1f NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H F2fF1F NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1
3D 1H-13C edited-filtered NOESY HSQC	sample_3	isotropic	sample_conditions_1
3D HCCH-COSY	sample_3	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1

Software:

Amber v21, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v3.1, Guntert, Mumenthaler and Wuthrich - structure calculation

CARA, Keller and Wuthrich - chemical shift assignment

ATNOS, Thorsten Hermann - peak picking

TopSpin, Bruker Biospin - collection

NMR spectrometers:

Bruker AVANCE III HD 900 MHz
Bruker AVANCE NEO 700 MHz
Bruker AVANCE NEO 600 MHz