BMRB Entry 17574

Name: Structure of a yeast RNase III dsRBD complex with a non-canonical RNA substrate provides new insights into substrate recognition
Published: 2011-08-03

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PDB ID: 2lbs
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17574
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Structure of a yeast RNase III dsRBD complex with a non-canonical RNA substrate provides new insights into substrate recognition

Deposition date: 2011-04-06 Original release date: 2011-08-03

Authors: Wang, Zhonghua; Hartman, Elon; Roy, Kevin; Chanfreau, Guillaume; Feigon, Juli

Citation: Wang, Zhonghua; Hartman, Elon; Roy, Kevin; Chanfreau, Guillaume; Feigon, Juli. "Structure of a yeast RNase III dsRBD complex with a non-canonical RNA substrate provides new insights into substrate recognition" Not known ., .-..

Assembly members:
yeast RNase III dsRBD, polymer, 90 residues, 9822.442 Da.
non-canonical RNA substrate, polymer, 32 residues, Formula weight is not available

Natural source: Common Name: baker Taxonomy ID: 4932 Superkingdom: not available Kingdom: not available Genus/species: Eukaryota Fungi

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
yeast RNase III dsRBD: GSLDMNAKRQLYSLIGYASL RLHYVTVKKPTAVDPNSIVE CRVGDGTVLGTGVGRNIKIA GIRAAENALRDKKMLDFYAK QRAAIPRSES
non-canonical RNA substrate: GGGAUACCAUGUUCAAGUGA ACGUGGUAUCUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	326
15N chemical shifts	87
1H chemical shifts	547

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	yeast RNase III dsRBD	1
2	non-canonical RNA substrate	2

Entities:

Entity 1, yeast RNase III dsRBD 90 residues - 9822.442 Da.

1	GLY	SER	LEU	ASP	MET	ASN	ALA	LYS	ARG	GLN
2	LEU	TYR	SER	LEU	ILE	GLY	TYR	ALA	SER	LEU
3	ARG	LEU	HIS	TYR	VAL	THR	VAL	LYS	LYS	PRO
4	THR	ALA	VAL	ASP	PRO	ASN	SER	ILE	VAL	GLU
5	CYS	ARG	VAL	GLY	ASP	GLY	THR	VAL	LEU	GLY
6	THR	GLY	VAL	GLY	ARG	ASN	ILE	LYS	ILE	ALA
7	GLY	ILE	ARG	ALA	ALA	GLU	ASN	ALA	LEU	ARG
8	ASP	LYS	LYS	MET	LEU	ASP	PHE	TYR	ALA	LYS
9	GLN	ARG	ALA	ALA	ILE	PRO	ARG	SER	GLU	SER

Entity 2, non-canonical RNA substrate 32 residues - Formula weight is not available

1

G

A

U

A

C

A

U

2

G

U

C

A

G

U

G

A

3

A

C

G

U

G

U

A

U

C

4

U

C

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 0.8 – 1 mM; entity_21 – 2 mM; NaCl 150 mM; phosphate buffer 20 mM

sample_2: entity_1, [U-100% 13C; U-100% 15N], 0.8 – 1 mM; entity_21 – 2 mM; NaCl 150 mM; phosphate buffer 20 mM

sample_3: entity_10.8 – 1 mM; entity_2, [U-100% 13C; U-100% 15N], 1 – 2 mM; NaCl 150 mM; phosphate buffer 20 mM

sample_4: entity_10.8 – 1 mM; entity_2, [U-100% 13C; U-100% 15N], 1 – 2 mM; NaCl 150 mM; phosphate buffer 20 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_4	isotropic	sample_conditions_1
2D FILTERED/EDITED NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC IPAP	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR NIH v2.24, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMRView v5.2.2, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

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

TALOS, Cornilescu, Delaglio and Bax - data analysis

TOPSPIN v2.0, Bruker Biospin - collection

xwinnmr, Bruker Biospin - collection

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

Bruker DRX 600 MHz
Bruker DRX 500 MHz

BMRB	18534 18535
PDB	1T4L 1T4N 1T4O 2LBS 2LUP 2LUQ 4OOG
DBJ	GAA25690
EMBL	CAA90210 CAY82070
GB	AAB04172 AHY76694 AJP40933 AJS62105 AJS62540
REF	NP_013966
SP	Q02555
TPG	DAA10139

Biological Magnetic Resonance Data Bank