BMRB Entry 25138

Name: Chemical shift assignments of DRB4(1-153), a dsRNA binding protein in A. thaliana RNAi pathway
Published: 2014-10-14

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PDB ID: 2n3f
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR25138
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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:

Chemical shift assignments of DRB4(1-153), a dsRNA binding protein in A. thaliana RNAi pathway

Deposition date:

2014-08-09

Original release date:

2014-10-14

Authors:

Deshmukh, Mandar V.; Chiliveri, Sai Chaitanya

Citation:

Citation: Chiliveri, Sai Chaitanya; Deshmukh, Mandar. "Chemical shift assignments of DRB4 (1-153), a dsRNA binding protein in A. thaliana RNAi pathway." Biomol NMR Assign 9, 253-256 (2015).
PubMed: 25281003

Assembly members:

Assembly members:
DRB4(1-153), polymer, 153 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Thale cress Taxonomy ID: 3702 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Arabidopsis thaliana

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-30a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DRB4(1-153): MDHVYKGQLQAYALQHNLEL PVYANEREGPPHAPRFRCNV TFCGQTFQSSEFFPTLKSAE HAAAKIAVASLTPQSPEGID VAYKNLLQEIAQKESSLLPF YATATSGPSHAPTFTSTVEF AGKVFSGEEAKTKKLAEMSA AKVAFMSIKNGNS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	559
15N chemical shifts	148
1H chemical shifts	951

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DRB4(1-153)	1

Entities:

Entity 1, DRB4(1-153) 153 residues - Formula weight is not available

1

MET

ASP

HIS

VAL

TYR

LYS

GLY

GLN

LEU

GLN

2

ALA

TYR

ALA

LEU

GLN

HIS

ASN

LEU

GLU

LEU

3

PRO

VAL

TYR

ALA

ASN

GLU

ARG

GLU

GLY

PRO

4

PRO

HIS

ALA

PRO

ARG

PHE

ARG

CYS

ASN

VAL

5

THR

PHE

CYS

GLY

GLN

THR

PHE

GLN

SER

6

GLU

PHE

PRO

THR

LEU

LYS

SER

ALA

GLU

7

HIS

ALA

LYS

ILE

ALA

VAL

ALA

SER

8

LEU

THR

PRO

GLN

SER

PRO

GLU

GLY

ILE

ASP

9

VAL

ALA

TYR

LYS

ASN

LEU

GLN

GLU

ILE

10

ALA

GLN

LYS

GLU

SER

LEU

PRO

PHE

11

TYR

ALA

THR

ALA

THR

SER

GLY

PRO

SER

HIS

12

ALA

PRO

THR

PHE

THR

SER

THR

VAL

GLU

PHE

13

ALA

GLY

LYS

VAL

PHE

SER

GLY

GLU

ALA

14

LYS

THR

LYS

LEU

ALA

GLU

MET

SER

ALA

15

ALA

LYS

VAL

ALA

PHE

MET

SER

ILE

LYS

ASN

16

GLY

ASN

SER

Samples:

15N: DRB4(1-153), [U-100% 15N], 0.5 mM; Potassium phosphate buffer 50 mM; Na2SO4 100 mM; DTT 4 mM

13C_15N: DRB4(1-153), [U-100% 13C; U-100% 15N], 0.5 mM; Potassium phosphate buffer 50 mM; Na2SO4 100 mM; DTT 4 mM

10_13C: DRB4(1-153), [U-10% 13C; U-100% 15N], 0.5 mM; Potassium phosphate buffer 50 mM; Na2SO4 100 mM; DTT 4 mM

15N_D2O: DRB4(1-153), [U-100% 15N], 0.5 mM; Potassium phosphate buffer 50 mM; Na2SO4 100 mM; DTT 4 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	15N	isotropic	sample_conditions_1
3D HNCO	13C_15N	isotropic	sample_conditions_1
3D HN(CA)CO	13C_15N	isotropic	sample_conditions_1
3D HNCA	13C_15N	isotropic	sample_conditions_1
3D HN(CO)CA	13C_15N	isotropic	sample_conditions_1
3D HNCACB	13C_15N	isotropic	sample_conditions_1
3D HN(CO)CACB	13C_15N	isotropic	sample_conditions_1
2D 1H-13C HSQC	13C_15N	isotropic	sample_conditions_1
3D H(CCO)NH-TOCSY	13C_15N	isotropic	sample_conditions_1
3D (H)C(CO)NH-TOCSY	13C_15N	isotropic	sample_conditions_1
3D HCCH-TOCSY	13C_15N	isotropic	sample_conditions_1
3D HNHA	13C_15N	isotropic	sample_conditions_1
3D HNHB	13C_15N	isotropic	sample_conditions_1
2D 1H-15N HSQC	15N_D2O	isotropic	sample_conditions_1
2D 1H-13C HSQC	10_13C	isotropic	sample_conditions_1
2D 1H-1H TOCSY	15N_D2O	isotropic	sample_conditions_1
2D 1H-1H NOESY	15N_D2O	isotropic	sample_conditions_1
3D 1H-15N NOESY	15N	isotropic	sample_conditions_1
3D 1H-13C NOESY	13C_15N	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1.6, Bruker Biospin - collection, processing

CARA, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

SPARKY, Goddard - data analysis

NMR spectrometers:

Bruker Avance 600 MHz

DBJ	BAG69145
GB	AAL67059 AAN13025 AEE80393 AEE80394 AEE80395
REF	NP_001154686 NP_191839 NP_974480
SP	Q8H1D4
AlphaFold	Q8H1D4