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BMRB: 15111

2JNH

Solution Structure of the UBA Domain from Cbl-b

Authors

Zhou, C., Zhou, Z., Lin, D., Hu, H.

Assembly

Cbl-b

Entity

1. Cbl-b (polymer, Thiol state: not present), 46 monomers, 5107.747 Da Detail

EAALENVDAK IAKLMGEGYA FEEVKRALEI AQNNVEVARS ILREFA

Formula weight

5107.747 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.5 %, Completeness: 67.3 %, Completeness (bb): 73.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	67.3 % (356 of 529)	72.6 % (199 of 274)	56.1 % (115 of 205)	84.0 % (42 of 50)
Backbone	73.9 % (204 of 276)	89.4 % (84 of 94)	57.4 % (78 of 136)	91.3 % (42 of 46)
Sidechain	63.3 % (188 of 297)	63.9 % (115 of 180)	64.6 % (73 of 113)	0.0 % (0 of 4)
Aromatic	0.0 % (0 of 28)	0.0 % (0 of 14)	0.0 % (0 of 14)
Methyl	79.0 % (49 of 62)	83.9 % (26 of 31)	74.2 % (23 of 31)

1. UBA domain of Cbl-b

EAALENVDAK IAKLMGEGYA FEEVKRALEI AQNNVEVARS ILREFA

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	entity	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2JNH, Strand ID: A Detail

Release date

2008-07-07

Citation

Differential ubiquitin binding of the UBA domains from human c-Cbl and Cbl-b: NMR structural and biochemical insights
Zhou, Z., Gao, H., Zhou, C., Chang, Y., Hong, J., Song, A., Lin, D., Hu, H.
Protein Sci. (2008), 17, 1805-1814, PubMed 18596201 , DOI 10.1110/ps.036384.108 , Abstract

Related entities 1. Cbl-b, : 1 : 5 : 2 : 1 : 16 entities Detail

Interaction partners 1. Cbl-b, : 34 interactors Detail

More details for 34 interactors identified by 20 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 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	entity	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 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	entity	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 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	entity	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %

4 3D C(CO)NH

Instrument

Varian INOVA - 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	entity	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %

5 3D HNCO

Instrument

Varian INOVA - 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	entity	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %

6 3D HNCACB

Instrument

Varian INOVA - 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	entity	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 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	entity	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %

8 3D HNHA

Instrument

Varian INOVA - 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	entity	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 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	entity	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %

10 3D 1H-13C NOESY

Instrument

Varian INOVA - 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	entity	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15111_2jnh.nef
Input source #2: Coordindates	2jnh.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------
EAALENVDAKIAKLMGEGYAFEEVKRALEIAQNNVEVARSILREFA
||||||||||||||||||||||||||||||||||||||||||||||
EAALENVDAKIAKLMGEGYAFEEVKRALEIAQNNVEVARSILREFA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	46	0	0	100.0

Content subtype: combined_15111_2jnh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	359		91.3 (chain: A, length: 46)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	567 (1)	noe	89.1 (chain: A, length: 46)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 46, Sequence coverage: 91.3%
- Total number of assignments
  - ¹H chemical shifts: 204
  - ¹⁵N chemical shifts: 42
  - ¹³C chemical shifts: 113
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 46, Sequence coverage: 89.1%
- Total number of restraints: 567
- Weight of restraints: 1.0 (567)
- Potential type of restraints: square-well-parabolic (567)
- Range of distance target values: 1.41, 5.21 (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 Cbl-b, NMR, UBA domain