BMRB Entry 25540

Name: NMR structure of the complex between the C-terminal domain of the Rift Valley fever virus protein NSs and the PH domain of the Tfb1 subunit of TFIIH.
Published: 2015-04-20

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PDB ID: 2n0y
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25540
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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:

NMR structure of the complex between the C-terminal domain of the Rift Valley fever virus protein NSs and the PH domain of the Tfb1 subunit of TFIIH.

Deposition date:

2015-03-18

Original release date:

2015-04-20

Authors:

Cyr, Normand; de la Fuente, Cynthia; Lecoq, Lauriane; Guendel, Irene; Chabot, Philippe; Kehn-Hall, Kylene; Omichinski, James

Citation:

Citation: Cyr, Normand; de la Fuente, Cynthia; Lecoq, Lauriane; Guendel, Irene; Chabot, Philippe; Kehn-Hall, Kylene; Omichinski, James. "A OmegaXaV motif in the Rift Valley fever virus NSs protein is essential for degrading p62, forming nuclear filaments and virulence." Proc. Natl. Acad. Sci. U.S.A. 112, 6021-6026 (2015).
PubMed: 25918396

Assembly members:

Assembly members:
RNA_polymerase_II_transcription_factor_B_subunit_1, polymer, 115 residues, 12903.807 Da.
Non-structural_protein_NS-S, polymer, 24 residues, 2566.504 Da.

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukarota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-2T

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_polymerase_II_transcription_factor_B_subunit_1: PSHSGAAIFEKVSGIIAINE DVSPAELTWRSTDGDKVHTV VLSTIDKLQATPASSEKMML RLIGKVDESKKRKDNEGNEV VPKPQRHMFSFNNRTVMDNI KMTLQQIISRYKDAD
Non-structural_protein_NS-S: GGGGYDVEMESEEESDDDGF VEVD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	597
15N chemical shifts	143
1H chemical shifts	953

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA polymerase II transcription factor B subunit 1	1
2	Non-structural protein NS-S	2

Entities:

Entity 1, RNA polymerase II transcription factor B subunit 1 115 residues - 12903.807 Da.

1

PRO

SER

HIS

SER

GLY

ALA

ILE

PHE

GLU

2

LYS

VAL

SER

GLY

ILE

ALA

ILE

ASN

GLU

3

ASP

VAL

SER

PRO

ALA

GLU

LEU

THR

TRP

ARG

4

SER

THR

ASP

GLY

ASP

LYS

VAL

HIS

THR

VAL

5

VAL

LEU

SER

THR

ILE

ASP

LYS

LEU

GLN

ALA

6

THR

PRO

ALA

SER

GLU

LYS

MET

LEU

7

ARG

LEU

ILE

GLY

LYS

VAL

ASP

GLU

SER

LYS

8

LYS

ARG

LYS

ASP

ASN

GLU

GLY

ASN

GLU

VAL

9

VAL

PRO

LYS

PRO

GLN

ARG

HIS

MET

PHE

SER

10

PHE

ASN

ARG

THR

VAL

MET

ASP

ASN

ILE

11

LYS

MET

THR

LEU

GLN

ILE

SER

ARG

12

TYR

LYS

ASP

ALA

ASP

Entity 2, Non-structural protein NS-S 24 residues - 2566.504 Da.

Residues 242-246 were introduced to faciliate the purification and quantification of the protein.

1

GLY

TYR

ASP

VAL

GLU

MET

GLU

2

SER

GLU

SER

ASP

GLY

PHE

3

VAL

GLU

VAL

ASP

Samples:

sample_1: RNA polymerase II transcription factor B subunit 1, [U-13C; U-15N], 1 mM; Non-structural protein NS-S 2 mM; H2O 90%; D2O 10%

sample_2: RNA polymerase II transcription factor B subunit 1, [U-13C; U-15N], 1 mM; Non-structural protein NS-S 2 mM; D2O 100%

sample_3: RNA polymerase II transcription factor B subunit 1, [U-15N], 0.5 mM; Non-structural protein NS-S 1 mM; H2O 90%; D2O 10%

sample_4: RNA polymerase II transcription factor B subunit 1 1 mM; Non-structural protein NS-S, [U-13C; U-15N], 0.5 mM; H2O 90%; D2O 10%

sample_5: RNA polymerase II transcription factor B subunit 1 0.5 mM; Non-structural protein NS-S, [U-13C; U-15N], 1 mM; D2O 100%

sample_6: RNA polymerase II transcription factor B subunit 1 0.4 mM; Non-structural protein NS-S, [U-15N], 0.2 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_6	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_4	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_5	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_5	isotropic	sample_conditions_1
3D 1H-13C NOESY intermolecular	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY intermolecular	sample_5	isotropic	sample_conditions_1

Software:

CcpNmr_Analysis v2.3.1 -

CNS -

TALOS-N -

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz

SP	P32776 P32776 P21698
REF	NP_010597 NP_010597 YP_003848706
BMRB	6225 18229 18842 19791
PDB	1y5o 1Y5O 2GS0 2K2U 2L2I 2LOX 2M14 2MKR 2N0Y
DBJ	GAA22531
EMBL	CAY78811
GB	AAA35143 AAB64747 AAU09707 AHY75284 AJP38011
TPG	DAA12150
AlphaFold	E9P948 P32776 A2SZX2