BMRB Entry 25436

Name: Solution structure of hnRNP C RRM in complex with the 5'-AUUUUUC-3' RNA
Published: 2015-02-23

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PDB ID: 2mxy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25436
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of hnRNP C RRM in complex with the 5'-AUUUUUC-3' RNA

Deposition date:

2015-01-19

Original release date:

2015-02-23

Authors:

Cienikova, Zuzana; Damberger, Fred; Hall, Jonathan; Allain, Frederic; Maris, Christophe

Citation:

Citation: Cienikova, Zuzana; Damberger, Fred; Hall, Jonathan; Allain, Frederic; Maris, Christophe. "Structural and mechanistic insights into poly(uridine) tract recognition by the hnRNP C RNA recognition motif." J. Am. Chem. Soc. 136, 14536-14544 (2014).
PubMed: 25216038

Assembly members:

Assembly members:
hnRNP_C, polymer, 105 residues, 11292.014 Da.
RNA_(5'-R(*AP*UP*UP*UP*UP*UP*C)-3'), polymer, 7 residues, 2120.276 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 Vector: pTYB11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
hnRNP_C: ASNVTNKTDPRSMNSRVFIG NLNTLVVKKSDVEAIFSKYG KIVGCSVHKGFAFVQYVNER NARAAVAGEDGRMIAGQVLD INLAAEPKVNRGKAGVKRSA AEMYG
RNA_(5'-R(*AP*UP*UP*UP*UP*UP*C)-3'): AUUUUUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	464
15N chemical shifts	117
1H chemical shifts	790

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	hnRNP_C	1
2	RNA (5'-R(APUPUPUPUPUP*C)-3')	2

Entities:

Entity 1, hnRNP_C 105 residues - 11292.014 Da.

1

ALA

SER

ASN

VAL

THR

ASN

LYS

THR

ASP

PRO

2

ARG

SER

MET

ASN

SER

ARG

VAL

PHE

ILE

GLY

3

ASN

LEU

ASN

THR

LEU

VAL

LYS

SER

4

ASP

VAL

GLU

ALA

ILE

PHE

SER

LYS

TYR

GLY

5

LYS

ILE

VAL

GLY

CYS

SER

VAL

HIS

LYS

GLY

6

PHE

ALA

PHE

VAL

GLN

TYR

VAL

ASN

GLU

ARG

7

ASN

ALA

ARG

ALA

VAL

ALA

GLY

GLU

ASP

8

GLY

ARG

MET

ILE

ALA

GLY

GLN

VAL

LEU

ASP

9

ILE

ASN

LEU

ALA

GLU

PRO

LYS

VAL

ASN

10

ARG

GLY

LYS

ALA

GLY

VAL

LYS

ARG

SER

ALA

11

ALA

GLU

MET

TYR

GLY

Entity 2, RNA (5'-R(*AP*UP*UP*UP*UP*UP*C)-3') 7 residues - 2120.276 Da.

1

A

U

C

Samples:

sample_1: hnRNP C, [U-100% 15N], 1.0 mM; RNA (5'-R(*AP*UP*UP*UP*UP*UP*C)-3') 1.0 mM; sodium phosphate 20 mM; sodium chloride 10 mM; H2O 90%; D2O 10%

sample_2: hnRNP C, [U-100% 13C; U-100% 15N], 1.0 mM; RNA (5'-R(*AP*UP*UP*UP*UP*UP*C)-3') 1.0 mM; sodium phosphate 20 mM; sodium chloride 10 mM; H2O 90%; D2O 10%

sample_3: hnRNP C, [U-100% 13C; U-100% 15N], 1.0 mM; RNA (5'-R(*AP*UP*UP*UP*UP*UP*C)-3') 1.0 mM; sodium phosphate 20 mM; sodium chloride 10 mM; D2O 100%

sample_4: hnRNP C, [U-100% 15N], 0.5 – 1.0 mM; RNA (5'-R(*AP*UP*UP*UP*UP*UP*C)-3'), [100% 13C5]-Ura, 0.5 – 1.0 mM; sodium phosphate 20 mM; sodium chloride 10 mM; D2O 100%

sample_conditions_1: ionic strength: 0.040 M; pH: 6.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C edited-filtered NOESY	sample_4	isotropic	sample_conditions_1
3D 1H-13C edited-filtered NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance 900 MHz
Bruker AVIII 600 MHz
Bruker AVIII 700 MHz
Bruker AVIII 500 MHz
Bruker AVIII 750 MHz

UNP	P07910
BMRB	25469
PDB	2MXY 2MZ1
DBJ	BAB27553 BAB28370 BAB31934 BAC40233 BAC40499
EMBL	CAD61934 CAD62326 CAH91328
GB	AAA36576 AAA52680 AAC61695 AAD03717 AAH03394
REF	NP_001029567 NP_001070910 NP_001070911 NP_001075507 NP_001125784
SP	G3V9R8 O77768 P07910 Q5RA82 Q9Z204
TPG	DAA25480
AlphaFold	Q9BTS3 G3V9R8 Q5RA82 P07910 O77768 Q9Z204