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BMRB: 18581

2LVN

Solution structure of gp78 CUE domain

Authors

Liu, S., Chen, Y., Huang, T., Tarasov, S.G., King, A., Li, J., Weissman, A.M., Byrd, R.A., Das, R.

Assembly

gp78 CUE domain

Entity

1. gp78 CUE domain (polymer, Thiol state: not present), 52 monomers, 5962.717 Da Detail

SNSQLNAMAH QIQEMFPQVP YHLVLQDLQL TRSVEITTDN ILEGRIQVPF PT

Formula weight

5962.717 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 92.5 %, Completeness (bb): 93.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.5 % (577 of 624)	89.8 % (292 of 325)	96.3 % (232 of 241)	91.4 % (53 of 58)
Backbone	93.1 % (283 of 304)	91.1 % (92 of 101)	94.2 % (146 of 155)	93.8 % (45 of 48)
Sidechain	92.2 % (342 of 371)	89.3 % (200 of 224)	97.8 % (134 of 137)	80.0 % (8 of 10)
Aromatic	100.0 % (36 of 36)	100.0 % (18 of 18)	100.0 % (18 of 18)
Methyl	100.0 % (68 of 68)	100.0 % (34 of 34)	100.0 % (34 of 34)

1. entity

SNSQLNAMAH QIQEMFPQVP YHLVLQDLQL TRSVEITTDN ILEGRIQVPF PT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 50 mM Tris pH 7.2 50mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		50 mM
2	sodium chloride	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.14 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.75 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LVN, Strand ID: C Detail

Release date

2012-11-18

Citation

Promiscuous interactions of gp78 E3 ligase CUE domain with polyubiquitin chains
Liu, S., Chen, Y., Li, J., Huang, T., Tarasov, S., King, A., Weissman, A.M., Byrd, R., Das, R.
Structure (2012), 20, 2138-2150, PubMed 23123110 , DOI 10.1016/j.str.2012.09.020 , Abstract

Related entities 1. gp78 CUE domain, : 1 : 5 : 2 : 2 : 24 entities Detail

Interaction partners 1. gp78 CUE domain, : 33 interactors Detail

More details for 33 interactors identified by 11 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 50 mM Tris pH 7.2 50mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		50 mM
2	sodium chloride	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 50 mM Tris pH 7.2 50mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		50 mM
2	sodium chloride	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Bruker INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 50 mM Tris pH 7.2 50mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		50 mM
2	sodium chloride	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D CBCA(CO)NH

Instrument

Bruker INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 50 mM Tris pH 7.2 50mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		50 mM
2	sodium chloride	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D C(CO)NH

Instrument

Bruker INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 50 mM Tris pH 7.2 50mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		50 mM
2	sodium chloride	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D H(CCO)NH

Instrument

Bruker INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 50 mM Tris pH 7.2 50mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		50 mM
2	sodium chloride	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D HNCACB

Instrument

Bruker INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 50 mM Tris pH 7.2 50mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		50 mM
2	sodium chloride	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 2D 1H-13C HSQC aromatic

Instrument

Bruker INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 50 mM Tris pH 7.2 50mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		50 mM
2	sodium chloride	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 50 mM Tris pH 7.2 50mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		50 mM
2	sodium chloride	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints	combined_18581_2lvn.nef
Input source #2: Coordindates	2lvn.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): C vs Auth_asym_ID (model): C

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
C	C	52	0	0	100.0

Content subtype: combined_18581_2lvn.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	590		96.2 (chain: C, length: 52)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	97 (97)	.	98.1 (chain: C, length: 52)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 52, Sequence coverage: 96.2%
- Total number of assignments
  - ¹H chemical shifts: 306
  - ¹³C chemical shifts: 231
  - ¹⁵N chemical shifts: 53
- Completeness of assignments
  - Entity_assemble_ID: C
- 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: C

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 52, Sequence coverage: 98.1%
- Total number of restraints: 97
- Total number of restraints per polymer type: 97
- Weight of restraints: 1.0 (97)
- Potential type of restraints: square-well-parabolic (97)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: C

Keywords CUE, gp78, NMR, Protein