BMRB Entry 25831

Name: solution structure of the complex of microRNA 20b pre-element with Rbfox RRM
Published: 2016-04-12

Click here to enlarge.

PDB ID: 2n82
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR25831
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

solution structure of the complex of microRNA 20b pre-element with Rbfox RRM

Deposition date:

2015-09-30

Original release date:

2016-04-12

Authors:

Yang, Fan; Chen, Yu; Varani, Gabriele

Citation:

Citation: Chen, Yu; Zubovic, Lorena; Yang, Fan; Godin, Katherine; Pavelitz, Tom; Castellanos, Javier; Macchi, Paolo; Varani, Gabriele. "Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer" Nucleic Acids Res. 44, 4381-4395 (2016).
PubMed: 27001519

Assembly members:

Assembly members:
miR-20b, polymer, 23 residues, 7318.388 Da.
Rbfox_RRM, polymer, 104 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: T7 in vitro transcription Host organism: NA Vector: NA

Entity Sequences (FASTA):

Entity Sequences (FASTA):
miR-20b: GGUAGUUUUGGCAUGACUCU ACC
Rbfox_RRM: GSHMNTENKSQPKRLHVSNI PFRFRDPDLRQMFGQFGKIL DVEIIFNERGSKGFGFVTFE NSADADRAREKLHGTVVEGR KIEVNNATARVMTNKKTVNP YTNG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	566
15N chemical shifts	115
1H chemical shifts	838

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	miR-20b	1
2	Rbfox_RRM	2

Entities:

Entity 1, miR-20b 23 residues - 7318.388 Da.

1

G

U

A

G

U

G

2

G

C

A

U

G

A

C

U

C

U

3

A

C

Entity 2, Rbfox_RRM 104 residues - Formula weight is not available

1

GLY

SER

HIS

MET

ASN

THR

GLU

ASN

LYS

SER

2

GLN

PRO

LYS

ARG

LEU

HIS

VAL

SER

ASN

ILE

3

PRO

PHE

ARG

PHE

ARG

ASP

PRO

ASP

LEU

ARG

4

GLN

MET

PHE

GLY

GLN

PHE

GLY

LYS

ILE

LEU

5

ASP

VAL

GLU

ILE

PHE

ASN

GLU

ARG

GLY

6

SER

LYS

GLY

PHE

GLY

PHE

VAL

THR

PHE

GLU

7

ASN

SER

ALA

ASP

ALA

ASP

ARG

ALA

ARG

GLU

8

LYS

LEU

HIS

GLY

THR

VAL

GLU

GLY

ARG

9

LYS

ILE

GLU

VAL

ASN

ALA

THR

ALA

ARG

10

VAL

MET

THR

ASN

LYS

THR

VAL

ASN

PRO

11

TYR

THR

ASN

GLY

Samples:

sample_1: miR-20b 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; Rbfox RRM, [U-99% 13C; U-99% 15N], 1 mM; H2O 90%; D2O 10%

sample_2: miR-20b 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; Rbfox RRM, [U-99% 13C; U-99% 15N], 1 mM; D2O 100%

sample_3: miR-20b, [U-99% 13C; U-99% 15N], 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; Rbfox RRM 1 mM; D2O 100%

sample_4: miR-20b, [U-99% 13C; U-99% 15N], 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; Rbfox RRM 1 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 279 K

sample_conditions_2: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D F1-, F2-filtered 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D F1-, F2-filtered 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_2
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_2
3D HNCACB	sample_1	isotropic	sample_conditions_2
3D HNCO	sample_1	isotropic	sample_conditions_2
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_2
3D CCH-TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
3D 13C F1-filtered, F3-edited NOESY-HSQC	sample_2	isotropic	sample_conditions_2

Software:

TOPSPIN, Bruker Biospin - collection

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

CcpNMR, CCPN - chemical shift assignment, data analysis, peak picking

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

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz