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Found 1 Document (1.045 seconds)

BMRB: 25132

5ISN

NMR study of non-structural proteins - 1H, 13C, 15N resonance assigment of macro domain of Venezuelan equine encephalitis virus (VEEV)

Authors

Makrynitsa, G.I., Ntonti, D., Marousis, K.D., Bentrop, D., Spyroulias, G.A.

Assembly

VEEV macro domain

Entity

1. VEEV macro domain (polymer, Thiol state: all free), 160 monomers, 17251.40 Da Detail

APSYHVVRGD IATATEGVII NAANSKGQPG GGVCGALYKK FPESFDLQPI EVGKARLVKG AAKHIIHAVG PNFNKVSEVE GDKQLAEAYE SIAKIVNDNN YKSVAIPLLS TGIFSGNKDR LTQSLNHLLT ALDTTDADVA IYCRDKKWEM TLKEAVARRE

Formula weight

17251.4 Da

Source organism

Venezuelan equine encephalitis virus

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 87.9 %, Completeness (bb): 94.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.9 % (1588 of 1806)	87.1 % (813 of 933)	89.5 % (631 of 705)	85.7 % (144 of 168)
Backbone	94.9 % (900 of 948)	93.3 % (305 of 327)	96.8 % (452 of 467)	92.9 % (143 of 154)
Sidechain	82.8 % (832 of 1005)	83.8 % (508 of 606)	83.9 % (323 of 385)	7.1 % (1 of 14)
Aromatic	5.6 % (6 of 108)	7.4 % (4 of 54)	3.8 % (2 of 53)	0.0 % (0 of 1)
Methyl	97.5 % (193 of 198)	98.0 % (97 of 99)	97.0 % (96 of 99)

1. VEEV macro domain

APSYHVVRGD IATATEGVII NAANSKGQPG GGVCGALYKK FPESFDLQPI EVGKARLVKG AAKHIIHAVG PNFNKVSEVE GDKQLAEAYE SIAKIVNDNN YKSVAIPLLS TGIFSGNKDR LTQSLNHLLT ALDTTDADVA IYCRDKKWEM TLKEAVARRE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	VEEV macro domain	[U-99% 15N]	0.4 mM
2	NaCl	natural abundance	20 mM
3	HEPES	natural abundance	10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details specific labeling with [U-15N]LEU-VAL-ALA

#	Name	Isotope labeling	Concentration
7	VEEV macro domain	[U-99% 15N]	0.01 mM
8	NaCl	natural abundance	20 mM
9	HEPES	natural abundance	10 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details reverse labeling [U-14N]LYS

#	Name	Isotope labeling	Concentration
10	VEEV macro domain	[U-99% 15N]	0.02 mM
11	NaCl	natural abundance	20 mM
12	HEPES	natural abundance	10 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	VEEV macro domain	natural abundance	0.3 mM
14	NaCl	natural abundance	20 mM
15	HEPES	natural abundance	10 mM

LACS Plot; CA

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

Referencing offset: 0.21 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.21 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.17 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 21 models in PDB: 5ISN, Strand ID: A Detail

Release date

2014-08-04

Citation

NMR study of non-structural proteins Part II: 1H, 13C, 15N backbone & side-chain resonance assignment of macro domain of Venezuelan equine encephalitis virus (VEEV)
Makrynitsa, G.I., Ntonti, D.I., Marousis, K.D., Bentrop, D., Spyroulias, G.A.
Biomol. NMR Assignments

Related entities 1. VEEV macro domain, : 1 : 5 : 1 : 129 entities Detail

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	VEEV macro domain	[U-99% 15N]	0.4 mM
2	NaCl	natural abundance	20 mM
3	HEPES	natural abundance	10 mM

2 2D 1H-15N HSQC

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details specific labeling with [U-15N]LEU-VAL-ALA

#	Name	Isotope labeling	Concentration
7	VEEV macro domain	[U-99% 15N]	0.01 mM
8	NaCl	natural abundance	20 mM
9	HEPES	natural abundance	10 mM

3 2D 1H-15N HSQC

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details reverse labeling [U-14N]LYS

#	Name	Isotope labeling	Concentration
10	VEEV macro domain	[U-99% 15N]	0.02 mM
11	NaCl	natural abundance	20 mM
12	HEPES	natural abundance	10 mM

4 2D 1H-1H NOESY

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	VEEV macro domain	natural abundance	0.3 mM
14	NaCl	natural abundance	20 mM
15	HEPES	natural abundance	10 mM

5 3D 1H-15N NOESY

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	VEEV macro domain	[U-99% 15N]	0.4 mM
2	NaCl	natural abundance	20 mM
3	HEPES	natural abundance	10 mM

6 3D CBCA(CO)NH

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

7 3D HNCACB

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

8 3D HNCO

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

9 3D HN(CA)CO

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

10 3D HNCA

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

11 3D HN(CO)CA

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

12 3D HBHA(CO)NH

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

13 3D HNHA

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	VEEV macro domain	[U-99% 15N]	0.4 mM
2	NaCl	natural abundance	20 mM
3	HEPES	natural abundance	10 mM

14 3D HCCH-TOCSY

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

15 2D 1H-13C HSQC

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

16 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

17 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance HD-III HD - 700 MHz equipped with TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	VEEV macro domain	[U-98% 13C; U-98% 15N]	0.8 mM
5	NaCl	natural abundance	20 mM
6	HEPES	natural abundance	10 mM

18 2D 1H-15N HSQC

Instrument

Bruker DPX - 400 MHz equipped with BBI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	VEEV macro domain	[U-99% 15N]	0.4 mM
2	NaCl	natural abundance	20 mM
3	HEPES	natural abundance	10 mM

19 2D 1H-1H TOCSY

Instrument

Bruker DPX - 400 MHz equipped with BBI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	VEEV macro domain	natural abundance	0.3 mM
14	NaCl	natural abundance	20 mM
15	HEPES	natural abundance	10 mM

20 2D 1H-1H NOESY

Instrument

Bruker DPX - 400 MHz equipped with BBI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	VEEV macro domain	natural abundance	0.3 mM
14	NaCl	natural abundance	20 mM
15	HEPES	natural abundance	10 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25132_5isn.nef
Input source #2: Coordindates	5isn.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

-0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------1
MKAPSYHVVRGDIATATEGVIINAANSKGQPGGGVCGALYKKFPESFDLQPIEVGKARLVKGAAKHIIHAVGPNFNKVSEVEGDKQLAEAYESIAKIVND
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKAPSYHVVRGDIATATEGVIINAANSKGQPGGGVCGALYKKFPESFDLQPIEVGKARLVKGAAKHIIHAVGPNFNKVSEVEGDKQLAEAYESIAKIVND
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

00-------110-------120-------130-------140-------150-------160------
NNYKSVAIPLLSTGIFSGNKDRLTQSLNHLLTALDTTDADVAIYCRDKKWEMTLKEAVARREHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NNYKSVAIPLLSTGIFSGNKDRLTQSLNHLLTALDTTDADVAIYCRDKKWEMTLKEAVARREHHHHHH
-------110-------120-------130-------140-------150-------160--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	168	0	0	100.0

Content subtype: combined_25132_5isn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1582		91.7 (chain: A, length: 168)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2319 (1)	noe	90.5 (chain: A, length: 168)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 168, Sequence coverage: 91.7%
- Total number of assignments
  - ¹H chemical shifts: 806
  - ¹³C chemical shifts: 629
  - ¹⁵N chemical shifts: 147
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	PRO	N	138.13
29	PRO	N	138.13
42	PRO	N	138.13
49	PRO	N	138.13
71	PRO	N	138.13
107	PRO	N	138.13

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	986	806	81.7
¹³C chemical shifts	746	629	84.3
¹⁵N chemical shifts	182	141	77.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	343	305	88.9
¹³C chemical shifts	336	308	91.7
¹⁵N chemical shifts	162	141	87.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	643	501	77.9
¹³C chemical shifts	410	321	78.3
¹⁵N chemical shifts	20	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	97	96.0
¹³C chemical shifts	101	96	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	0	0.0
¹³C chemical shifts	65	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 168, Sequence coverage: 90.5%
- Total number of restraints: 2295
- Weight of restraints: 1.0 (2295)
- Potential type of restraints: upper-bound-parabolic (2295)
- Range of distance target values: 2.4, 10.22 (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 ADP-ribose-binding module, NMR spectroscopy, Selective aminoacid labeling, VEEV, Venezuelan equine encephalitis virus, alphavirus, recombinant protein expression, viral macro domains

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Found 1 Document (1.045 seconds)

BMRB: 25132

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. VEEV macro domain, : 1 : 5 : 1 : 129 entities Detail

Experiments performed 20 experiments Detail

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NMR combined restraints 3 contents Detail