BMRB Entry 34151

Name: Solution structure of the complexed RCD1-RST
Published: 2018-04-13

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PDB ID: 5oao
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34151
MolProbity Validation Chart

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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 the complexed RCD1-RST

Deposition date: 2017-06-23 Original release date: 2018-04-13

Authors: Bugge, K.; Staby, L.; Skriver, K.; Kragelund, B.

Citation: Bugge, K.; Staby, L.; Kemplen, K.; Bendsen, S.; Jensen, M.; Olsen, J.; Skriver, K.; Kragelund, B.. "The alpha-alpha-hub domains: PAH, TAFH, NCBD and RST; A novel hub-family in transcriptional networks" . ., .-..

Assembly members:
RST domain from the Radical-Induced Cell Death1, polymer, 73 residues, 8455.854 Da.

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

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

Entity Sequences (FASTA):
RST domain from the Radical-Induced Cell Death1: TTRPKSPWMPFPTLFAAISH KVAENDMLLINADYQQLRDK KMTRAEFVRKLRVIVGDDLL RSTITTLQNQPKS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	245
15N chemical shifts	60
1H chemical shifts	381

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 73 residues - 8455.854 Da.

1

THR

ARG

PRO

LYS

SER

PRO

TRP

MET

PRO

2

PHE

PRO

THR

LEU

PHE

ALA

ILE

SER

HIS

3

LYS

VAL

ALA

GLU

ASN

ASP

MET

LEU

ILE

4

ASN

ALA

ASP

TYR

GLN

LEU

ARG

ASP

LYS

5

LYS

MET

THR

ARG

ALA

GLU

PHE

VAL

ARG

LYS

6

LEU

ARG

VAL

ILE

VAL

GLY

ASP

LEU

7

ARG

SER

THR

ILE

THR

LEU

GLN

ASN

GLN

8

PRO

LYS

SER

Samples:

sample_1: DREB2A 200 uM; DSS 0.7 mM; RCD1-RST, [U-13C; U-15N], 200 uM; sodium azide 0.2 mg/mL; NaCl 100 mM

sample_2: DREB2A 150 uM; DSS 0.7 mM; RCD1-RST, [U-15N], 150 uM; sodium azide 0.2 mg/mL; NaCl 100 mM

sample_3: DREB2A, [U-13C; U-15N], 200 uM; DSS 0.7 mM; RCD1-RST, [U-13C; U-15N], 200 uM; sodium azide 0.2 mg/mL; NaCl 100 mM

sample_4: C12E5 50 mg/mL; DREB2A 900 uM; DSS 0.7 mM; RCD1-RST, [U-15N], 300 uM; sodium azide 0.2 mg/mL; NaCl 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N 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 HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_3	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1
2D 1H-15N IPAP-HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N IPAP-HSQC	sample_4	anisotropic	sample_conditions_1

Software:

Analysis, CCPN - chemical shift assignment, data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

ProcheckNMR, Laskowski and MacArthur - geometry optimization

TALOS, Cornilescu, Delaglio and Bax - data analysis

TOPSPIN, Bruker Biospin - collection

VNMR, Varian - collection

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Varian INOVA 800 MHz
Varian INOVA 750 MHz
Bruker Avance 750 MHz
Bruker Avance 600 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts