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BMRB: 15618

2JZD

NMR ASSIGNMENT OF THE DOMAIN 527-651 OF THE SARS-COV NONSTRUCTURAL PROTEIN NSP3

Authors

Chatterjee, A., Johnson, M.A., Serrano, P., Pedrini, B., Joseph, J., Saikatendu, K., Neuman, B., Stevens, R.C., Wilson, I.A., Buchmeier, M.J., Kuhn, P., Wuthrich, K.

Assembly

nsp3(527-651)

Entity

1. nsp3(527-651) (polymer, Thiol state: all free), 129 monomers, 14349.53 Da Detail

GSHMGTVSWN LREMLAHAEE TRKLMPICMD VRAIMATIQR KYKGIKIQEG IVDYGVRFFF YTSKEPVASI ITKLNSLNEP LVTMPIGYVT HGFNLEEAAR CMRSLKAPAV VSVSSPDAVT TYNGYLTSS

Formula weight

14349.53 Da

Source organism

Severe acute respiratory syndrome-related coronavirus

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 92.0 %, Completeness (bb): 88.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.0 % (1371 of 1491)	98.2 % (755 of 769)	82.2 % (486 of 591)	99.2 % (130 of 131)
Backbone	88.6 % (675 of 762)	98.8 % (257 of 260)	78.1 % (296 of 379)	99.2 % (122 of 123)
Sidechain	96.1 % (817 of 850)	97.8 % (498 of 509)	93.4 % (311 of 333)	100.0 % (8 of 8)
Aromatic	76.8 % (86 of 112)	92.9 % (52 of 56)	60.0 % (33 of 55)	100.0 % (1 of 1)
Methyl	100.0 % (156 of 156)	100.0 % (78 of 78)	100.0 % (78 of 78)

1. nsp3(527-651)

GSHMGTVSWN LREMLAHAEE TRKLMPICMD VRAIMATIQR KYKGIKIQEG IVDYGVRFFF YTSKEPVASI ITKLNSLNEP LVTMPIGYVT HGFNLEEAAR CMRSLKAPAV VSVSSPDAVT TYNGYLTSS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.22 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.22 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.34 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2008-01-06

Citation

Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold
Chatterjee, A., Johnson, M.A., Serrano, P., Pedrini, B., Joseph, J.S., Neuman, B.W., Saikatendu, K., Buchmeier, M.J., Kuhn, P., Wuthrich, K.
J. Virol. (2009), 83, 1823-1836, PubMed 19052085 , DOI 10.1128/JVI.01781-08 , Abstract

Related entities 1. nsp3(527-651), : 1 : 3 : 18 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

3 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

4 3D 1H-15N TOCSY

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

5 3D 1H-13C NOESY aliphatic region

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

6 3D 1H-13C NOESY aromatic region

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

8 4D APSY-HNCOCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

9 4D APSY-HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

10 5D APSY-CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

11 5D APSY-HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp3(527-651)	[U-99% 13C; U-98% 15N]		1.4 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	sodium azide	natural abundance		2 mM
5	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15618_2jzd.nef
Input source #2: Coordindates	2jzd.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

-----530-------540-------550-------560-------570-------580-------590-------600-------610-------620--
GSHMGTVSWNLREMLAHAEETRKLMPICMDVRAIMATIQRKYKGIKIQEGIVDYGVRFFFYTSKEPVASIITKLNSLNEPLVTMPIGYVTHGFNLEEAAR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMGTVSWNLREMLAHAEETRKLMPICMDVRAIMATIQRKYKGIKIQEGIVDYGVRFFFYTSKEPVASIITKLNSLNEPLVTMPIGYVTHGFNLEEAAR
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----630-------640-------650-
CMRSLKAPAVVSVSSPDAVTTYNGYLTSS
|||||||||||||||||||||||||||||
CMRSLKAPAVVSVSSPDAVTTYNGYLTSS
-------110-------120---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	129	0	0	100.0

Content subtype: combined_15618_2jzd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1366		99.2 (chain: A, length: 129)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2908 (1)	noe	98.4 (chain: A, length: 129)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 129, Sequence coverage: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 755
  - ¹³C chemical shifts: 481
  - ¹⁵N chemical shifts: 130
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 129, Sequence coverage: 98.4%
- Total number of restraints: 2908
- Weight of restraints: 1.0 (2908)
- Potential type of restraints: upper-bound-parabolic (2908)
- Range of distance target values: 2.4, 5.5 (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 SARS-CoV, SARS-unique domain, nonstructural protein, nsp3, nsp3c