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BMRB: 27356

5ZD0

1H, 13C, and 15N Chemical Shift Assignments for ubiquitin in sf9 cells by in-cell NMR spectroscopy

Authors

Tanaka, T., Ikeya, T., Kamoshida, H., Mishima, M., Shirakawa, M., Guentert, P., Ito, Y.

Assembly

ubiquitin 3A mutants

Entity

1. ubiquitin 3A mutants (polymer, Thiol state: all free), 76 monomers, 8452.518 Da Detail

MQIFVKTATG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLAFAGKQL EDGRTLSDYN IQKESTLHLA LRLRGG

Formula weight

8452.518 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.7 %, Completeness: 56.0 %, Completeness (bb): 64.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	56.0 % (499 of 891)	66.0 % (309 of 468)	34.8 % (119 of 342)	87.7 % (71 of 81)
Backbone	64.7 % (291 of 450)	94.2 % (146 of 155)	33.3 % (74 of 222)	97.3 % (71 of 73)
Sidechain	42.3 % (216 of 511)	52.1 % (163 of 313)	27.9 % (53 of 190)	0.0 % (0 of 8)
Aromatic	56.3 % (18 of 32)	75.0 % (12 of 16)	37.5 % (6 of 16)
Methyl	92.4 % (85 of 92)	93.5 % (43 of 46)	91.3 % (42 of 46)

1. ubiquitin3A

MQIFVKTATG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLAFAGKQL EDGRTLSDYN IQKESTLHLA LRLRGG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin3A	[U-100% 15N]		50 (±12.0) uM
2	ubiquitin3A	[U-100% 13C; U-100% 15N]		50 (±12.0) uM

Protein Blocks Logo

Calculated from 20 models in PDB: 5ZD0, Strand ID: A Detail

Release date

2018-01-10

Citation

High-Resolution Protein 3D Structure Determination in Living Eukaryotic Cells
Tanaka, T., Ikeya, T., Kamoshida, H., Suemoto, Y., Mishima, M., Shirakawa, M., Guntert, P., Ito, Y.
Angew. Chem Int Ed Engl. (2019), 58, 7284-7288, PubMed 30938016 , DOI 10.1002/anie.201900840 , Abstract

Related entities 1. ubiquitin 3A mutants, : 1 : 385 : 333 entities Detail

Interaction partners 1. ubiquitin 3A mutants, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin3A	[U-100% 15N]		50 (±12.0) uM
2	ubiquitin3A	[U-100% 13C; U-100% 15N]		50 (±12.0) uM

2 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin3A	[U-100% 15N]		50 (±12.0) uM
2	ubiquitin3A	[U-100% 13C; U-100% 15N]		50 (±12.0) uM

3 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin3A	[U-100% 15N]		50 (±12.0) uM
2	ubiquitin3A	[U-100% 13C; U-100% 15N]		50 (±12.0) uM

4 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin3A	[U-100% 15N]		50 (±12.0) uM
2	ubiquitin3A	[U-100% 13C; U-100% 15N]		50 (±12.0) uM

5 3D HN(CO)CA

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin3A	[U-100% 15N]		50 (±12.0) uM
2	ubiquitin3A	[U-100% 13C; U-100% 15N]		50 (±12.0) uM

6 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin3A	[U-100% 15N]		50 (±12.0) uM
2	ubiquitin3A	[U-100% 13C; U-100% 15N]		50 (±12.0) uM

7 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin3A	[U-100% 15N]		50 (±12.0) uM
2	ubiquitin3A	[U-100% 13C; U-100% 15N]		50 (±12.0) uM

8 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin3A	[U-100% 15N]		50 (±12.0) uM
2	ubiquitin3A	[U-100% 13C; U-100% 15N]		50 (±12.0) uM

9 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin3A	[U-100% 15N]		50 (±12.0) uM
2	ubiquitin3A	[U-100% 13C; U-100% 15N]		50 (±12.0) uM

10 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin3A	[U-100% 15N]		50 (±12.0) uM
2	ubiquitin3A	[U-100% 13C; U-100% 15N]		50 (±12.0) uM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr27356_3.str
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	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr27356_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	572		98.7 (chain: 1, length: 76)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 76, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 393
  - ¹³C chemical shifts: 109
  - ¹⁵N chemical shifts: 70
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Keywords in-cell NMR, protein structure determination, sf9 cell