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Found 1 Document (0.607 seconds)

BMRB: 19003

2M4H

Solution structure of the Core Domain (10-76) of the Feline Calicivirus VPg protein.

Authors

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

Assembly

Core Domain (10-76) of the Feline Calicivirus VPg protein

Entity

1. Core Domain (10-76) of the Feline Calicivirus VPg protein (polymer, Thiol state: not present), 71 monomers, 8350.040 Da Detail

IGTYRGRGVA LTDDEYDEWR EHNASRKLDL SVEDFLMLRH RAALGADDND AVKFRSWWNS RTKMANDYED V

Formula weight

8350.04 Da

Source organism

Feline calicivirus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.1 %, Completeness (bb): 98.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.1 % (778 of 818)	93.4 % (396 of 424)	96.5 % (305 of 316)	98.7 % (77 of 78)
Backbone	98.4 % (419 of 426)	97.9 % (143 of 146)	98.1 % (205 of 209)	100.0 % (71 of 71)
Sidechain	92.6 % (425 of 459)	91.0 % (253 of 278)	95.4 % (166 of 174)	85.7 % (6 of 7)
Aromatic	96.6 % (85 of 88)	95.5 % (42 of 44)	97.6 % (40 of 41)	100.0 % (3 of 3)
Methyl	93.8 % (60 of 64)	93.8 % (30 of 32)	93.8 % (30 of 32)

1. FCV VPg

IGTYRGRGVA LTDDEYDEWR EHNASRKLDL SVEDFLMLRH RAALGADDND AVKFRSWWNS RTKMANDYED V

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details 100-200 uM protein in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3

#	Name	Isotope labeling	Concentration
1	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
2	sodium chloride	natural abundance	300 mM
3	HEPES pH7	natural abundance	20 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details Protein: 100-200 M in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3.

#	Name	Isotope labeling	Concentration
7	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
8	sodium chloride	natural abundance	300 mM
9	sodium azide	natural abundance	1 mM
10	HEPES pH7	natural abundance	20 mM
11	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details Protein: 100-200 M in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3.

#	Name	Isotope labeling	Concentration
12	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
13	sodium chloride	natural abundance	300 mM
14	sodium azide	natural abundance	1 mM
15	HEPES pH7	natural abundance	20 mM
16	Pf1 phage	natural abundance	15 mg/mL
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

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: -0.07 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: -0.07 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: 0.06 ppm, Outliers: 3 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: -0.21 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M4H, Strand ID: A Detail

Release date

2013-02-12

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

Entries sharing articles BMRB: 1 entries Detail

BMRB: 19002 released on 2013-03-20
Title Solution structure of the Core Domain (11-85) of the Murine Norovirus VPg protein.

Related entities 1. Core Domain (10-76) of the Feline Calicivirus VPg protein, : 1 : 1 : 20 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details 100-200 uM protein in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3

#	Name	Isotope labeling	Concentration
1	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
2	sodium chloride	natural abundance	300 mM
3	HEPES pH7	natural abundance	20 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 3D HNCACB

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details 100-200 uM protein in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3

#	Name	Isotope labeling	Concentration
1	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
2	sodium chloride	natural abundance	300 mM
3	HEPES pH7	natural abundance	20 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details 100-200 uM protein in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3

#	Name	Isotope labeling	Concentration
1	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
2	sodium chloride	natural abundance	300 mM
3	HEPES pH7	natural abundance	20 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

4 3D HNCO

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details 100-200 uM protein in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3

#	Name	Isotope labeling	Concentration
1	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
2	sodium chloride	natural abundance	300 mM
3	HEPES pH7	natural abundance	20 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

5 3D HBHA(CBCACO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details 100-200 uM protein in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3

#	Name	Isotope labeling	Concentration
1	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
2	sodium chloride	natural abundance	300 mM
3	HEPES pH7	natural abundance	20 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

6 3D 1H-15N NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details 100-200 uM protein in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3

#	Name	Isotope labeling	Concentration
1	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
2	sodium chloride	natural abundance	300 mM
3	HEPES pH7	natural abundance	20 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

7 3D HCCH-TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 283 K, pH 7, Details Protein: 100-200 M in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3.

#	Name	Isotope labeling	Concentration
7	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
8	sodium chloride	natural abundance	300 mM
9	sodium azide	natural abundance	1 mM
10	HEPES pH7	natural abundance	20 mM
11	D2O	natural abundance	100 %

8 3D 1H-13C NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 283 K, pH 7, Details Protein: 100-200 M in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3.

#	Name	Isotope labeling	Concentration
7	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
8	sodium chloride	natural abundance	300 mM
9	sodium azide	natural abundance	1 mM
10	HEPES pH7	natural abundance	20 mM
11	D2O	natural abundance	100 %

9 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 283 K, pH 7, Details Protein: 100-200 M in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3.

#	Name	Isotope labeling	Concentration
7	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
8	sodium chloride	natural abundance	300 mM
9	sodium azide	natural abundance	1 mM
10	HEPES pH7	natural abundance	20 mM
11	D2O	natural abundance	100 %

10 2D 1H-13C HSQC aliphatic

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 283 K, pH 7, Details Protein: 100-200 M in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3.

#	Name	Isotope labeling	Concentration
7	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
8	sodium chloride	natural abundance	300 mM
9	sodium azide	natural abundance	1 mM
10	HEPES pH7	natural abundance	20 mM
11	D2O	natural abundance	100 %

11 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 280 K, pH 7, Details Protein: 100-200 M in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3.

#	Name	Isotope labeling	Concentration
12	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
13	sodium chloride	natural abundance	300 mM
14	sodium azide	natural abundance	1 mM
15	HEPES pH7	natural abundance	20 mM
16	Pf1 phage	natural abundance	15 mg/mL
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

12 3D HN(CA)CO

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details 100-200 uM protein in 20 mM HEPES pH 7, 300 mM NaCl, 1 mM NaN3

#	Name	Isotope labeling	Concentration
1	FCV VPg 7-76	[U-99% 13C; U-99% 15N]	100.0 ~ 200.0 uM
2	sodium chloride	natural abundance	300 mM
3	HEPES pH7	natural abundance	20 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, RDC restraints	combined_19003_2m4h.nef
Input source #2: Coordindates	2m4h.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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	71	0	0	100.0

Content subtype: combined_19003_2m4h.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	793		100.0 (chain: A, length: 71)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1926 (1)	noe	94.4 (chain: A, length: 71)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	37 (37)	.	52.1 (chain: A, length: 71)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 405
  - ¹³C chemical shifts: 307
  - ¹⁵N chemical shifts: 81
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
48	HIS	HE2	7.85

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	424	404	95.3
¹³C chemical shifts	316	307	97.2
¹⁵N chemical shifts	86	81	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	146	144	98.6
¹³C chemical shifts	142	141	99.3
¹⁵N chemical shifts	71	70	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	278	260	93.5
¹³C chemical shifts	174	166	95.4
¹⁵N chemical shifts	15	11	73.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	30	88.2
¹³C chemical shifts	34	30	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	42	95.5
¹³C chemical shifts	41	40	97.6
¹⁵N chemical shifts	3	3	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 94.4%
- Total number of restraints: 1926
- Weight of restraints: 1.0 (1926)
- Potential type of restraints: square-well-parabolic (1926)
- Range of distance target values: 1.5, 3.7 (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

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 52.1%

-10-------20--------30--------40--------50--------60--------70---------
IGTYRGRGVALTDDEYDEWREHNASRKLDLSVEDFLMLRHRAALGADDNDAVKFRSWWNSRTKMANDYEDV
           || |||    |||| ||| |||| |||||||| |||||||   || ||||          
...........TD.EYD....HNAS.KLD.SVED.LMLRHRAA.GADDNDA...RS.WNSR          
-10-------20--------30--------40--------50--------60---------

Total number of restraints: 37
Potential type of restraints: undefined (37)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords Feline Calicivirus, NS5, VPg, Viral Protein genome linked

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Found 1 Document (0.607 seconds)

BMRB: 19003

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Core Domain (10-76) of the Feline Calicivirus VPg protein, : 1 : 1 : 20 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 4 contents Detail