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BMRB: 18583

2LVP

Solution structure of the gp78CUE/K48-Ub2 complex

Authors

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

Assembly

gp78CUE/K48-Ub2 complex

Entity

1. ubiquitin (polymer, Thiol state: not present), 76 monomers, 8564.731 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

2. gp78CUE (polymer, Thiol state: not present), 52 monomers, 5962.717 Da Detail

SNSQLNAMAH QIQEMFPQVP YHLVLQDLQL TRSVEITTDN ILEGRIQVPF PT

Total weight

14527.448 Da

Max. entity weight

8564.731 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.3 %, Completeness: 25.6 %, Completeness (bb): 60.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	25.6 % (241 of 942)	15.9 % (128 of 803)	81.3 % (113 of 139)
Backbone	60.7 % (229 of 377)	45.3 % (116 of 256)	93.4 % (113 of 121)
Sidechain	2.1 % (12 of 565)	2.2 % (12 of 547)	0.0 % (0 of 18)
Aromatic	0.0 % (0 of 34)	0.0 % (0 of 34)
Methyl	6.0 % (5 of 83)	6.0 % (5 of 83)

1. ubiquitin

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

2. gp78CUE

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 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LVP, Strand ID: A, B, 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. ubiquitin, : 92 : 6 : 46 : 182 entities Detail

Related entities 2. gp78CUE, : 1 : 5 : 2 : 2 : 24 entities Detail

Interaction partners 2. gp78CUE, : 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, Distance restraints	combined_18583_2lvp.nef
Input source #2: Coordindates	2lvp.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--------50--------60--------70------
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20--------30--------40--------50--------60--------70------
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Entity_assembly_ID (NMR): C vs Auth_asym_ID (model): C

-----460-------470-------480-------490-------500----
SNSQLNAMAHQIQEMFPQVPYHLVLQDLQLTRSVEITTDNILEGRIQVPFPT
||||||||||||||||||||||||||||||||||||||||||||||||||||
SNSQLNAMAHQIQEMFPQVPYHLVLQDLQLTRSVEITTDNILEGRIQVPFPT
--------10--------20--------30--------40--------50--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	76	0	0	100.0
B	B	76	0	0	100.0
C	C	52	0	0	100.0

Content subtype: combined_18583_2lvp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	gp78CUE_amides_in_gp78-K48Ub2	Warning	222		86.8 (chain: A, length: 76), 86.5 (chain: C, length: 52)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	45 (1)	noe	14.5 (chain: A, length: 76), 21.2 (chain: C, length: 52)

Assigned chemical shifts

Saveframe: gp78CUE_amides_in_gp78-K48Ub2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 86.8%
  - Entity_assembly_ID: C, Chain length: 52, Sequence coverage: 86.5%
- Total number of assignments
  - ¹H chemical shifts: 111
  - ¹⁵N chemical shifts: 111
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: C
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: C

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 14.5%
  - Entity_assembly_ID: C, Chain length: 52, Sequence coverage: 21.2%
- Total number of restraints: 45
- Weight of restraints: 1.0 (45)
- Potential type of restraints: square-well-parabolic (45)
- Range of distance target values: 0.67, 7.6 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
- Distance restraints on contact map

Keywords CUE, gp78, NMR, Protein