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BMRB: 25461

2MYX

Structure of the CUE domain of yeast Cue1

Authors

Kniss, A., Rogov, V.V., Loehr, F., Guentert, P., Doetsch, V.

Assembly

CUE domain of yeast Cue1

Entity

1. CUE domain of yeast Cue1 (polymer, Thiol state: not present), 75 monomers, 8257.977 Da Detail

GAMGPQGSTQ NALRRTGRVN GGHPVTTQMV ETVQNLAPNL HPEQIRYSLE NTGSVEETVE RYLRGDEFSF PPGFE

Formula weight

8257.977 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.7 %, Completeness: 96.3 %, Completeness (bb): 97.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (808 of 839)	97.5 % (428 of 439)	95.0 % (305 of 321)	94.9 % (75 of 79)
Backbone	97.7 % (428 of 438)	97.4 % (149 of 153)	98.1 % (212 of 216)	97.1 % (67 of 69)
Sidechain	95.3 % (445 of 467)	97.6 % (279 of 286)	92.4 % (158 of 171)	80.0 % (8 of 10)
Aromatic	81.5 % (44 of 54)	100.0 % (27 of 27)	63.0 % (17 of 27)
Methyl	97.1 % (66 of 68)	100.0 % (34 of 34)	94.1 % (32 of 34)

1. Coupling of ubiquitin conjugation to ER degradation protein 1 (Cue1)

GAMGPQGSTQ NALRRTGRVN GGHPVTTQMV ETVQNLAPNL HPEQIRYSLE NTGSVEETVE RYLRGDEFSF PPGFE

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

LACS Plot; CA

Referencing offset: -0.25 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.25 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.05 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.44 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2016-03-20

Citation

Dynamic binding of a ubiquitin binding domain to polyubiquitin stimulates chain elongation by an E2 enzyme
von Delbrueck, M., Kniss, A., Rogov, V.V., Pluska, L., Bagola, K., Loehr, F., Guentert, P., Sommer, T., Doetsch, V.
Not known

Related entities 1. CUE domain of yeast Cue1, : 1 : 2 : 7 entities Detail

Interaction partners 1. CUE domain of yeast Cue1, : 11 interactors Detail

More details for 11 interactors identified by 5 citations

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

2 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

5 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

6 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

7 3D long range 1H-15N TROSY HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

8 3D HN(CA)CO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

9 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

10 2D 1H-13C ct TROSY H(C)N

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

11 2D (H)CB(CG)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

12 2D (HB)CB(CGCD)HD

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

13 3D H(CC)(CO)NH TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

14 3D (H)C(C)(CO)NH TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

15 2D 1H-15N BEST TROSY H(N)N

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		100 mM
3	D2O	natural abundance		5 %
4	sodium azide	natural abundance		0.01 %
5	protease inhibitor cocktail	natural abundance		4.6 mM
6	CUE domain of Cue1	[U-98% 13C; U-98% 15N]		1.2 mM
7	DSS	natural abundance		100 uM
8	H2O	natural abundance		95 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25461_2myx.nef
Input source #2: Coordindates	2myx.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

--------50--------60--------70--------80--------90-------100-------110-----
GAMGPQGSTQNALRRTGRVNGGHPVTTQMVETVQNLAPNLHPEQIRYSLENTGSVEETVERYLRGDEFSFPPGFE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMGPQGSTQNALRRTGRVNGGHPVTTQMVETVQNLAPNLHPEQIRYSLENTGSVEETVERYLRGDEFSFPPGFE
--------10--------20--------30--------40--------50--------60--------70-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	75	0	0	100.0

Content subtype: combined_25461_2myx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	813		98.7 (chain: A, length: 75)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2155 (1)	noe	96.0 (chain: A, length: 75)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	36 (1)	hbond	41.3 (chain: A, length: 75)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	92 (92)	.	69.3 (chain: A, length: 75)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 427
  - ¹³C chemical shifts: 305
  - ¹⁵N chemical shifts: 81
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: 75, Sequence coverage: 96.0%
- Total number of restraints: 2155
- Weight of restraints: 1.0 (2155)
- Potential type of restraints: upper-bound-parabolic (2155)
- 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
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 41.3%
  - Total number of restraints: 36
  - Weight of restraints: 1.0 (36)
  - Potential type of restraints: upper-bound-parabolic (36)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 69.3%
- Total number of restraints: 92
- Total number of restraints per polymer type: 92
- Weight of restraints: 1.0 (92)
- Potential type of restraints: square-well-parabolic (92)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CUE domain, ERAD, ubiquitination