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BMRB: 25793

2N74

Solution Structure of the RNA-Binding domain of non-structural protein 1 from the 1918 H1N1 influenza virus

Authors

Jureka, A.S., Kleinpeter, A.B., Cornilescu, G., Cornilescu, C.C., Schwieters, C.D., Petit, C.M.

Assembly

RNA-Binding domain of non-structural protein 1 from the 1918 H1N1 influenza virus

Entity

1. RNA-Binding domain of non-structural protein 1 from the 1918 H1N1 influenza virus (polymer), 73 monomers, 8395.380 Da Detail

MDSNTVSSFQ VDCFLWHVRK RFADQELGDA PFLDRLRRDQ KSLRGRGSTL GLDIETATRA GKQIVERILK EES

Formula weight

8395.38 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 89.6 %, Completeness (bb): 97.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.6 % (769 of 858)	85.6 % (386 of 451)	94.5 % (311 of 329)	92.3 % (72 of 78)
Backbone	97.7 % (426 of 436)	98.0 % (147 of 150)	97.7 % (209 of 214)	97.2 % (70 of 72)
Sidechain	83.7 % (410 of 490)	79.4 % (239 of 301)	92.3 % (169 of 183)	33.3 % (2 of 6)
Aromatic	82.1 % (46 of 56)	100.0 % (28 of 28)	63.0 % (17 of 27)	100.0 % (1 of 1)
Methyl	98.7 % (75 of 76)	97.4 % (37 of 38)	100.0 % (38 of 38)

1. Influenza NS1 RNA Binding Domain

MDSNTVSSFQ VDCFLWHVRK RFADQELGDA PFLDRLRRDQ KSLRGRGSTL GLDIETATRA GKQIVERILK EES

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Influenza NS1 RNA Binding Domain	[U-13C; U-15N]		1.0 mM
2	Ammonium Acetate pH 6.0	natural abundance		300 mM
3	EDTA	natural abundance		2.2 mM
4	sodium azide	natural abundance		0.1 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
7	Influenza NS1 RNA Binding Domain	[U-15N]		1 mM
8	Ammonium Acetate pH 6.0	natural abundance		300 mM
9	EDTA	natural abundance		2.0 mM
10	sodium azide	natural abundance		0.1 %
11	H2O	natural abundance		95 %
12	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 16 models in PDB: 2N74, Strand ID: A, B Detail

Release date

2015-09-27

Citation

Structural Basis for a Novel Interaction between the NS1 Protein Derived from the 1918 Influenza Virus and RIG-I
Jureka, A.S., Kleinpeter, A.B., Cornilescu, G., Cornilescu, C.C., Schwieters, C.D., Petit, C.M.
Structure (2015), 23, 2001-2010, PubMed 26365801 , DOI 10.1016/j.str.2015.08.007 , Abstract

Related entities 1. RNA-Binding domain of non-structural protein 1 from the 1918 H1N1 influenza virus, : 1 : 3 : 24 : 7 : 86 entities Detail

Interaction partners 1. RNA-Binding domain of non-structural protein 1 from the 1918 H1N1 influenza virus, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Influenza NS1 RNA Binding Domain	[U-13C; U-15N]		1.0 mM
2	Ammonium Acetate pH 6.0	natural abundance		300 mM
3	EDTA	natural abundance		2.2 mM
4	sodium azide	natural abundance		0.1 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 3D HNCACB

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Influenza NS1 RNA Binding Domain	[U-13C; U-15N]		1.0 mM
2	Ammonium Acetate pH 6.0	natural abundance		300 mM
3	EDTA	natural abundance		2.2 mM
4	sodium azide	natural abundance		0.1 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Influenza NS1 RNA Binding Domain	[U-13C; U-15N]		1.0 mM
2	Ammonium Acetate pH 6.0	natural abundance		300 mM
3	EDTA	natural abundance		2.2 mM
4	sodium azide	natural abundance		0.1 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Influenza NS1 RNA Binding Domain	[U-13C; U-15N]		1.0 mM
2	Ammonium Acetate pH 6.0	natural abundance		300 mM
3	EDTA	natural abundance		2.2 mM
4	sodium azide	natural abundance		0.1 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 3D HNHA

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Influenza NS1 RNA Binding Domain	[U-13C; U-15N]		1.0 mM
2	Ammonium Acetate pH 6.0	natural abundance		300 mM
3	EDTA	natural abundance		2.2 mM
4	sodium azide	natural abundance		0.1 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 3D HCCH-COSY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Influenza NS1 RNA Binding Domain	[U-13C; U-15N]		1.0 mM
2	Ammonium Acetate pH 6.0	natural abundance		300 mM
3	EDTA	natural abundance		2.2 mM
4	sodium azide	natural abundance		0.1 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Influenza NS1 RNA Binding Domain	[U-13C; U-15N]		1.0 mM
2	Ammonium Acetate pH 6.0	natural abundance		300 mM
3	EDTA	natural abundance		2.2 mM
4	sodium azide	natural abundance		0.1 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Influenza NS1 RNA Binding Domain	[U-13C; U-15N]		1.0 mM
2	Ammonium Acetate pH 6.0	natural abundance		300 mM
3	EDTA	natural abundance		2.2 mM
4	sodium azide	natural abundance		0.1 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Influenza NS1 RNA Binding Domain	[U-13C; U-15N]		1.0 mM
2	Ammonium Acetate pH 6.0	natural abundance		300 mM
3	EDTA	natural abundance		2.2 mM
4	sodium azide	natural abundance		0.1 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_25793_2n74.nef
Input source #2: Coordindates	2n74.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70---
MDSNTVSSFQVDCFLWHVRKRFADQELGDAPFLDRLRRDQKSLRGRGSTLGLDIETATRAGKQIVERILKEES
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDSNTVSSFQVDCFLWHVRKRFADQELGDAPFLDRLRRDQKSLRGRGSTLGLDIETATRAGKQIVERILKEES

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

-------110-------120-------130-------140-------150-------160-------170---
MDSNTVSSFQVDCFLWHVRKRFADQELGDAPFLDRLRRDQKSLRGRGSTLGLDIETATRAGKQIVERILKEES
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDSNTVSSFQVDCFLWHVRKRFADQELGDAPFLDRLRRDQKSLRGRGSTLGLDIETATRAGKQIVERILKEES
--------10--------20--------30--------40--------50--------60--------70---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	73	0	0	100.0
B	B	73	0	0	100.0

Content subtype: combined_25793_2n74.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	766		98.6 (chain: A, length: 73)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 384
  - ¹³C chemical shifts: 311
  - ¹⁵N chemical shifts: 71
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Keywords NMR, NS1, RIG-I, influenza, virulence