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BMRB: 27506

6NFW

Chemical shift assignment of the viral protein genome-linked (VPg) from Potato virus Y

Authors

Coutinho de Oliveira, L., Volpon, L., Osborne, M.J., Borden, K.L.B.

Assembly

VPg

Entity

1. VPg (polymer, Thiol state: all free), 153 monomers, 17430.47 Da Detail

GSSAYRKKGK GKGTTVGMGK SSRRFINMYG FDPTEYSFIQ FVDPLTGAQI EENVYADIRD IQERFSEVRK KMVENDDIEM QALGSNTTIH AYFRKDWSDK ALKIDLMPHN PLKVCDKTNG IAKFPERELE LRQTGPAVEV DVKDIPAQEV EHE

Formula weight

17430.47 Da

Source organism

Potato virus Y

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 86.3 %, Completeness: 71.5 %, Completeness (bb): 79.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.5 % (1290 of 1805)	67.8 % (643 of 949)	73.9 % (515 of 697)	83.0 % (132 of 159)
Backbone	79.6 % (720 of 904)	76.1 % (236 of 310)	80.6 % (361 of 448)	84.2 % (123 of 146)
Sidechain	65.4 % (682 of 1043)	63.2 % (404 of 639)	68.8 % (269 of 391)	69.2 % (9 of 13)
Aromatic	47.0 % (63 of 134)	64.2 % (43 of 67)	28.8 % (19 of 66)	100.0 % (1 of 1)
Methyl	89.4 % (127 of 142)	90.1 % (64 of 71)	88.7 % (63 of 71)

1. VPg from potato virus Y

GSSAYRKKGK GKGTTVGMGK SSRRFINMYG FDPTEYSFIQ FVDPLTGAQI EENVYADIRD IQERFSEVRK KMVENDDIEM QALGSNTTIH AYFRKDWSDK ALKIDLMPHN PLKVCDKTNG IAKFPERELE LRQTGPAVEV DVKDIPAQEV EHE

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	1 mM
5	sodium azide	natural abundance	0.02 % v/v

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	150 mM
9	DTT	natural abundance	1 mM
10	sodium azide	natural abundance	0.02 % v/v

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
11	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	150 mM
14	DTT	natural abundance	1 mM
15	sodium azide	natural abundance	0.02 % v/v

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
16	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	150 mM
19	DTT	natural abundance	1 mM
20	sodium azide	natural abundance	0.02 % v/v

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.14 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 6NFW, Strand ID: A Detail

Release date

2018-06-05

Citation

Chemical shift assignment of the viral protein genome-linked (VPg) from potato virus Y
Coutinho de Oliveira, L., Volpon, L., Osborne, M.J., Borden, K.L.B.
Biomol. NMR Assign. (2018), 13, 9-13, PubMed 30242622 , DOI 10.1007/s12104-018-9842-3 , Abstract

Related entities 1. VPg, : 1 : 27 entities Detail

Experiments performed 21 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	1 mM
5	sodium azide	natural abundance	0.02 % v/v

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	150 mM
9	DTT	natural abundance	1 mM
10	sodium azide	natural abundance	0.02 % v/v

3 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	150 mM
9	DTT	natural abundance	1 mM
10	sodium azide	natural abundance	0.02 % v/v

4 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
16	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	150 mM
19	DTT	natural abundance	1 mM
20	sodium azide	natural abundance	0.02 % v/v

5 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
16	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	150 mM
19	DTT	natural abundance	1 mM
20	sodium azide	natural abundance	0.02 % v/v

6 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	1 mM
5	sodium azide	natural abundance	0.02 % v/v

7 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	1 mM
5	sodium azide	natural abundance	0.02 % v/v

8 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	1 mM
5	sodium azide	natural abundance	0.02 % v/v

9 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	1 mM
5	sodium azide	natural abundance	0.02 % v/v

10 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	1 mM
5	sodium azide	natural abundance	0.02 % v/v

11 3D HN(CA)CO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	1 mM
5	sodium azide	natural abundance	0.02 % v/v

12 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	150 mM
9	DTT	natural abundance	1 mM
10	sodium azide	natural abundance	0.02 % v/v

13 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	150 mM
9	DTT	natural abundance	1 mM
10	sodium azide	natural abundance	0.02 % v/v

14 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	150 mM
9	DTT	natural abundance	1 mM
10	sodium azide	natural abundance	0.02 % v/v

15 3D HN(CA)CO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	150 mM
9	DTT	natural abundance	1 mM
10	sodium azide	natural abundance	0.02 % v/v

16 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
11	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	150 mM
14	DTT	natural abundance	1 mM
15	sodium azide	natural abundance	0.02 % v/v

17 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	1 mM
5	sodium azide	natural abundance	0.02 % v/v

18 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	150 mM
9	DTT	natural abundance	1 mM
10	sodium azide	natural abundance	0.02 % v/v

19 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	VPg from potato virus Y	[U-100% 13C; U-100% 15N]	400 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	1 mM
5	sodium azide	natural abundance	0.02 % v/v

20 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
11	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	150 mM
14	DTT	natural abundance	1 mM
15	sodium azide	natural abundance	0.02 % v/v

21 3D (H)N(COCA)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	VPg from potato virus Y	[U-13C; U-15N; U-2H]	400 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	150 mM
9	DTT	natural abundance	1 mM
10	sodium azide	natural abundance	0.02 % v/v

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_27506_6nfw.nef
Input source #2: Coordindates	6nfw.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--------80--------90-------100
GKNKSKRIQALKFRHARDKRAGFEIDNNDDTIEEFFGSAYRKKGKGKGTTVGMGKSSRRFINMYGFDPTEYSFIQFVDPLTGAQIEENVYADIRDIQERF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GKNKSKRIQALKFRHARDKRAGFEIDNNDDTIEEFFGSAYRKKGKGKGTTVGMGKSSRRFINMYGFDPTEYSFIQFVDPLTGAQIEENVYADIRDIQERF

-------110-------120-------130-------140-------150-------160-------170-------180--------
SEVRKKMVENDDIEMQALGSNTTIHAYFRKDWSDKALKIDLMPHNPLKVCDKTNGIAKFPERELELRQTGPAVEVDVKDIPAQEVEHE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SEVRKKMVENDDIEMQALGSNTTIHAYFRKDWSDKALKIDLMPHNPLKVCDKTNGIAKFPERELELRQTGPAVEVDVKDIPAQEVEHE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	188	0	0	100.0

Content subtype: combined_27506_6nfw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1175		66.5 (chain: A, length: 188)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1166 (1)	noe	55.9 (chain: A, length: 188)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	58 (1)	hbond	19.7 (chain: A, length: 188)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 188, Sequence coverage: 66.5%
- Total number of assignments
  - ¹H chemical shifts: 571
  - ¹³C chemical shifts: 481
  - ¹⁵N chemical shifts: 123
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1184	571	48.2
¹³C chemical shifts	862	481	55.8
¹⁵N chemical shifts	211	123	58.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	382	215	56.3
¹³C chemical shifts	376	233	62.0
¹⁵N chemical shifts	181	115	63.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	802	356	44.4
¹³C chemical shifts	486	248	51.0
¹⁵N chemical shifts	30	8	26.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	66	75.0
¹³C chemical shifts	88	64	72.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	38	42.7
¹³C chemical shifts	88	17	19.3
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 188, Sequence coverage: 55.9%
- Total number of restraints: 1166
- Weight of restraints: 1.0 (1166)
- Potential type of restraints: upper-bound-parabolic (1166)
- Range of distance target values: 2.4, 9.0 (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
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 188, Sequence coverage: 19.7%
  - Total number of restraints: 58
  - Weight of restraints: 1.0 (58)
  - Potential type of restraints: upper-bound-parabolic (58)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

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Found 1 Document (0.569 seconds)

BMRB: 27506

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. VPg, : 1 : 27 entities Detail

Experiments performed 21 experiments Detail

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NMR combined restraints 4 contents Detail