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Found 1 Document (0.652 seconds)

BMRB: 19002

2M4G

Solution structure of the Core Domain (11-85) of the Murine Norovirus VPg protein.

Authors

Leen, E.N., Kwok, R., Birtley, J.R., Prater, S.N., Simpson, P.J., Matthews, S., Marchant, J., Curry, S.

Assembly

Core Domain (11-85) of the Murine Norovirus VPg protein

Entity

1. Core Domain (11-85) of the Murine Norovirus VPg protein (polymer, Thiol state: not present), 75 monomers, 8857.623 Da Detail

GRPGVFRTRG LTDEEYDEFK KRRESRGGKY SIDDYLADRE REEELLERDE EEAIFGDGFG LKATRRSRKA ERAKL

Formula weight

8857.623 Da

Source organism

Murine norovirus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.2 %, Completeness (bb): 100.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.2 % (860 of 885)	96.2 % (456 of 474)	97.9 % (330 of 337)	100.0 % (74 of 74)
Backbone	100.0 % (448 of 448)	100.0 % (157 of 157)	100.0 % (217 of 217)	100.0 % (74 of 74)
Sidechain	95.0 % (479 of 504)	94.3 % (299 of 317)	96.3 % (180 of 187)
Aromatic	78.1 % (50 of 64)	78.1 % (25 of 32)	78.1 % (25 of 32)
Methyl	100.0 % (52 of 52)	100.0 % (26 of 26)	100.0 % (26 of 26)

1. MNV VPg

GRPGVFRTRG LTDEEYDEFK KRRESRGGKY SIDDYLADRE REEELLERDE EEAIFGDGFG LKATRRSRKA ERAKL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 300 mM NaCl, 50 mM NaPO4 pH 6.5, 1 mM DTT.

#	Name	Isotope labeling	Concentration
1	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	590 uM
2	sodium phosphate	natural abundance	50 mM
3	Sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 36 mM NaCl, 60 mM NaPO4 pH 6.5, 1 mM DTT, 0.1% w/v NaN3, 1x roche PI.

#	Name	Isotope labeling	Concentration
7	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	710 uM
8	sodium chloride	natural abundance	360 mM
9	sodium azide	natural abundance	0.1 w/v
10	DTT	natural abundance	1 mM
11	sodium phosphate pH 6.5	natural abundance	60 mM
12	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	indirect	0.1013291

Referencing offset: -0.23 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	indirect	0.1013291

Referencing offset: -0.23 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M4G, Strand ID: A Detail

Release date

2013-03-20

Citation

Structures of the compact helical core domains of feline calicivirus and murine norovirus VPg proteins
Leen, E.N., Kwok, K., Birtley, J.R., Simpson, P.J., Subba-Reddy, C.V., Chaudhry, Y., Sosnovtsev, S.V., Green, K.Y., Prater, S.N., Tong, M., Young, J.C., Chung, L.M.W., Marchant, J., Roberts, L.O., Kao, C., Matthews, S., Goodfellow, I.G., Curry, S.
J. Virol. (2013), 87, 5318-5330, PubMed 23487472 , DOI 10.1128/JVI.03151-12 , Abstract

Related entities 1. Core Domain (11-85) of the Murine Norovirus VPg protein, : 1 : 4 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 300 mM NaCl, 50 mM NaPO4 pH 6.5, 1 mM DTT.

#	Name	Isotope labeling	Concentration
1	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	590 uM
2	sodium phosphate	natural abundance	50 mM
3	Sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 3D H(C)CH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 Pa, Temperature 303 K, pH 6.5, Details 36 mM NaCl, 60 mM NaPO4 pH 6.5, 1 mM DTT, 0.1% w/v NaN3, 1x roche PI.

#	Name	Isotope labeling	Concentration
7	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	710 uM
8	sodium chloride	natural abundance	360 mM
9	sodium azide	natural abundance	0.1 w/v
10	DTT	natural abundance	1 mM
11	sodium phosphate pH 6.5	natural abundance	60 mM
12	D2O	natural abundance	100 %

3 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 Pa, Temperature 303 K, pH 6.5, Details 36 mM NaCl, 60 mM NaPO4 pH 6.5, 1 mM DTT, 0.1% w/v NaN3, 1x roche PI.

#	Name	Isotope labeling	Concentration
7	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	710 uM
8	sodium chloride	natural abundance	360 mM
9	sodium azide	natural abundance	0.1 w/v
10	DTT	natural abundance	1 mM
11	sodium phosphate pH 6.5	natural abundance	60 mM
12	D2O	natural abundance	100 %

4 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 Pa, Temperature 303 K, pH 6.5, Details 36 mM NaCl, 60 mM NaPO4 pH 6.5, 1 mM DTT, 0.1% w/v NaN3, 1x roche PI.

#	Name	Isotope labeling	Concentration
7	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	710 uM
8	sodium chloride	natural abundance	360 mM
9	sodium azide	natural abundance	0.1 w/v
10	DTT	natural abundance	1 mM
11	sodium phosphate pH 6.5	natural abundance	60 mM
12	D2O	natural abundance	100 %

5 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 Pa, Temperature 303 K, pH 6.5, Details 36 mM NaCl, 60 mM NaPO4 pH 6.5, 1 mM DTT, 0.1% w/v NaN3, 1x roche PI.

#	Name	Isotope labeling	Concentration
7	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	710 uM
8	sodium chloride	natural abundance	360 mM
9	sodium azide	natural abundance	0.1 w/v
10	DTT	natural abundance	1 mM
11	sodium phosphate pH 6.5	natural abundance	60 mM
12	D2O	natural abundance	100 %

6 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 300 mM NaCl, 50 mM NaPO4 pH 6.5, 1 mM DTT.

#	Name	Isotope labeling	Concentration
1	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	590 uM
2	sodium phosphate	natural abundance	50 mM
3	Sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 300 mM NaCl, 50 mM NaPO4 pH 6.5, 1 mM DTT.

#	Name	Isotope labeling	Concentration
1	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	590 uM
2	sodium phosphate	natural abundance	50 mM
3	Sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

8 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 300 mM NaCl, 50 mM NaPO4 pH 6.5, 1 mM DTT.

#	Name	Isotope labeling	Concentration
1	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	590 uM
2	sodium phosphate	natural abundance	50 mM
3	Sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

9 3D HN(CA)CO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 300 mM NaCl, 50 mM NaPO4 pH 6.5, 1 mM DTT.

#	Name	Isotope labeling	Concentration
1	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	590 uM
2	sodium phosphate	natural abundance	50 mM
3	Sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

10 3D H(CC)(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 300 mM NaCl, 50 mM NaPO4 pH 6.5, 1 mM DTT.

#	Name	Isotope labeling	Concentration
1	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	590 uM
2	sodium phosphate	natural abundance	50 mM
3	Sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

11 3D (H)C(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 300 mM NaCl, 50 mM NaPO4 pH 6.5, 1 mM DTT.

#	Name	Isotope labeling	Concentration
1	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	590 uM
2	sodium phosphate	natural abundance	50 mM
3	Sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

12 3D (HB)CB(CGCD)HD

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 Pa, Temperature 303 K, pH 6.5, Details 36 mM NaCl, 60 mM NaPO4 pH 6.5, 1 mM DTT, 0.1% w/v NaN3, 1x roche PI.

#	Name	Isotope labeling	Concentration
7	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	710 uM
8	sodium chloride	natural abundance	360 mM
9	sodium azide	natural abundance	0.1 w/v
10	DTT	natural abundance	1 mM
11	sodium phosphate pH 6.5	natural abundance	60 mM
12	D2O	natural abundance	100 %

13 3D (HB)CB(CGCDCE)HE

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 Pa, Temperature 303 K, pH 6.5, Details 36 mM NaCl, 60 mM NaPO4 pH 6.5, 1 mM DTT, 0.1% w/v NaN3, 1x roche PI.

#	Name	Isotope labeling	Concentration
7	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	710 uM
8	sodium chloride	natural abundance	360 mM
9	sodium azide	natural abundance	0.1 w/v
10	DTT	natural abundance	1 mM
11	sodium phosphate pH 6.5	natural abundance	60 mM
12	D2O	natural abundance	100 %

14 3D HBHA(CBCACO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 300 mM NaCl, 50 mM NaPO4 pH 6.5, 1 mM DTT.

#	Name	Isotope labeling	Concentration
1	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	590 uM
2	sodium phosphate	natural abundance	50 mM
3	Sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

15 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 Pa, Temperature 303 K, pH 6.5, Details 36 mM NaCl, 60 mM NaPO4 pH 6.5, 1 mM DTT, 0.1% w/v NaN3, 1x roche PI.

#	Name	Isotope labeling	Concentration
7	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	710 uM
8	sodium chloride	natural abundance	360 mM
9	sodium azide	natural abundance	0.1 w/v
10	DTT	natural abundance	1 mM
11	sodium phosphate pH 6.5	natural abundance	60 mM
12	D2O	natural abundance	100 %

16 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 300 mM NaCl, 50 mM NaPO4 pH 6.5, 1 mM DTT.

#	Name	Isotope labeling	Concentration
1	MNV VPg 11-85	[U-98% 13C; U-98% 15N]	590 uM
2	sodium phosphate	natural abundance	50 mM
3	Sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19002_2m4g.nef
Input source #2: Coordindates	2m4g.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	Warning

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

--------20--------30--------40--------50--------60--------70--------80-----
GRPGVFRTRGLTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAIFGDGFGLKATRRSRKAERAKL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GRPGVFRTRGLTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAIFGDGFGLKATRRSRKAERAKL
--------10--------20--------30--------40--------50--------60--------70-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	75	0	0	100.0

Content subtype: combined_19002_2m4g.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	860		100.0 (chain: A, length: 75)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2744 (1)	noe	100.0 (chain: A, length: 75)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 455
  - ¹³C chemical shifts: 330
  - ¹⁵N chemical shifts: 75
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	474	454	95.8
¹³C chemical shifts	337	330	97.9
¹⁵N chemical shifts	87	75	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	157	156	99.4
¹³C chemical shifts	150	150	100.0
¹⁵N chemical shifts	74	74	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	317	298	94.0
¹³C chemical shifts	187	180	96.3
¹⁵N chemical shifts	13	1	7.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	26	100.0
¹³C chemical shifts	26	26	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	25	78.1
¹³C chemical shifts	32	25	78.1

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 100.0%
- Total number of restraints: 2743
- Weight of restraints: 1.0 (2743)
- Potential type of restraints: square-well-parabolic (2743)
- Range of distance target values: 1.4, 4.04 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Murine norovirus, NS5, Viral Proteinn genome linked, VPg

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Found 1 Document (0.652 seconds)

BMRB: 19002

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Core Domain (11-85) of the Murine Norovirus VPg protein, : 1 : 4 entities Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 3 contents Detail