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BMRB: 17828

2LGY

Ubiquitin-like domain from HOIL-1

Authors

Beasley, S.A., Shaw, G.S., Beasley, S.A.

Assembly

HOIL-1 Unl

Entity

1. HOIL-1 Unl (polymer, Thiol state: not present), 90 monomers, 10343.68 Da Detail

MPTQDIRLWV SVEDAQMHTV TIWLTVRPDM TVASLKDMVF LDYGFPPVLQ QWVIGQRLAR DQETLHSHGV RQNGDSAYLY LLSARNTSLN

Formula weight

10343.68 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.9 %, Completeness: 93.2 %, Completeness (bb): 93.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.2 % (989 of 1061)	94.0 % (513 of 546)	92.5 % (385 of 416)	91.9 % (91 of 99)
Backbone	93.6 % (498 of 532)	95.6 % (172 of 180)	92.1 % (245 of 266)	94.2 % (81 of 86)
Sidechain	93.0 % (572 of 615)	93.2 % (341 of 366)	93.6 % (221 of 236)	76.9 % (10 of 13)
Aromatic	97.8 % (90 of 92)	97.8 % (45 of 46)	100.0 % (43 of 43)	66.7 % (2 of 3)
Methyl	98.3 % (114 of 116)	100.0 % (58 of 58)	96.6 % (56 of 58)

1. HOIL-1 Ubl

MPTQDIRLWV SVEDAQMHTV TIWLTVRPDM TVASLKDMVF LDYGFPPVLQ QWVIGQRLAR DQETLHSHGV RQNGDSAYLY LLSARNTSLN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	HOIL-1 Ubl	[U-15N]		0.2 mM
2	potassium phosphate	natural abundance		10 mM
3	EDTA	natural abundance		1 mM
4	potassium chloride	natural abundance		50 mM
5	DSS	natural abundance		30 uM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
8	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
9	potassium phosphate	natural abundance		10 mM
10	EDTA	natural abundance		1 mM
11	potassium chloride	natural abundance		50 mM
12	DSS	natural abundance		30 uM
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
15	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
16	potassium phosphate	natural abundance		10 mM
17	EDTA	natural abundance		1 mM
18	potassium chloride	natural abundance		50 mM
19	DSS	natural abundance		30 uM
20	D2O	natural abundance		100 %

LACS Plot; CA

Referencing offset: 0.01 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.01 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.26 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2012-04-29

Citation

Solution structure of the E3 ligase HOIL-1 Ubl domain
Beasley, S.A., Safadi, S.S., Barber, K.R., Shaw, G.S.
Protein Sci. (2012), 21, 1085-1092, PubMed 22517668 , DOI 10.1002/pro.2080 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: Q9BYM8 released on 2001-09-26
Title HOIL1_HUMAN Entity RanBP-type and C3HC4-type zinc finger-containing protein 1

Related entities 1. HOIL-1 Unl, : 1 : 4 : 22 entities Detail

Interaction partners 1. HOIL-1 Unl, : 47 interactors Detail

More details for 47 interactors identified by 16 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	HOIL-1 Ubl	[U-15N]		0.2 mM
2	potassium phosphate	natural abundance		10 mM
3	EDTA	natural abundance		1 mM
4	potassium chloride	natural abundance		50 mM
5	DSS	natural abundance		30 uM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 3D HNCO

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
8	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
9	potassium phosphate	natural abundance		10 mM
10	EDTA	natural abundance		1 mM
11	potassium chloride	natural abundance		50 mM
12	DSS	natural abundance		30 uM
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

3 3D HN(CA)CO

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
8	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
9	potassium phosphate	natural abundance		10 mM
10	EDTA	natural abundance		1 mM
11	potassium chloride	natural abundance		50 mM
12	DSS	natural abundance		30 uM
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

4 3D HNCA

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
8	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
9	potassium phosphate	natural abundance		10 mM
10	EDTA	natural abundance		1 mM
11	potassium chloride	natural abundance		50 mM
12	DSS	natural abundance		30 uM
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

5 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
8	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
9	potassium phosphate	natural abundance		10 mM
10	EDTA	natural abundance		1 mM
11	potassium chloride	natural abundance		50 mM
12	DSS	natural abundance		30 uM
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

6 3D HNCACB

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
8	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
9	potassium phosphate	natural abundance		10 mM
10	EDTA	natural abundance		1 mM
11	potassium chloride	natural abundance		50 mM
12	DSS	natural abundance		30 uM
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

7 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
8	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
9	potassium phosphate	natural abundance		10 mM
10	EDTA	natural abundance		1 mM
11	potassium chloride	natural abundance		50 mM
12	DSS	natural abundance		30 uM
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

8 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
8	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
9	potassium phosphate	natural abundance		10 mM
10	EDTA	natural abundance		1 mM
11	potassium chloride	natural abundance		50 mM
12	DSS	natural abundance		30 uM
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

9 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
8	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
9	potassium phosphate	natural abundance		10 mM
10	EDTA	natural abundance		1 mM
11	potassium chloride	natural abundance		50 mM
12	DSS	natural abundance		30 uM
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

10 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
15	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
16	potassium phosphate	natural abundance		10 mM
17	EDTA	natural abundance		1 mM
18	potassium chloride	natural abundance		50 mM
19	DSS	natural abundance		30 uM
20	D2O	natural abundance		100 %

11 3D HCCH-COSY aromatic

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
15	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
16	potassium phosphate	natural abundance		10 mM
17	EDTA	natural abundance		1 mM
18	potassium chloride	natural abundance		50 mM
19	DSS	natural abundance		30 uM
20	D2O	natural abundance		100 %

12 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
15	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
16	potassium phosphate	natural abundance		10 mM
17	EDTA	natural abundance		1 mM
18	potassium chloride	natural abundance		50 mM
19	DSS	natural abundance		30 uM
20	D2O	natural abundance		100 %

13 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
15	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
16	potassium phosphate	natural abundance		10 mM
17	EDTA	natural abundance		1 mM
18	potassium chloride	natural abundance		50 mM
19	DSS	natural abundance		30 uM
20	D2O	natural abundance		100 %

14 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
15	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
16	potassium phosphate	natural abundance		10 mM
17	EDTA	natural abundance		1 mM
18	potassium chloride	natural abundance		50 mM
19	DSS	natural abundance		30 uM
20	D2O	natural abundance		100 %

15 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
15	HOIL-1 Ubl	[U-13C; U-15N]		0.2 mM
16	potassium phosphate	natural abundance		10 mM
17	EDTA	natural abundance		1 mM
18	potassium chloride	natural abundance		50 mM
19	DSS	natural abundance		30 uM
20	D2O	natural abundance		100 %

16 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz 13C-enhanced triple resonance cold probe with z-gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	HOIL-1 Ubl	[U-15N]		0.2 mM
2	potassium phosphate	natural abundance		10 mM
3	EDTA	natural abundance		1 mM
4	potassium chloride	natural abundance		50 mM
5	DSS	natural abundance		30 uM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17828_2lgy.nef
Input source #2: Coordindates	2lgy.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--------80--------90
MPTQDIRLWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLLSARNTSLN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MPTQDIRLWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLLSARNTSLN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	90	0	0	100.0

Content subtype: combined_17828_2lgy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	992		98.9 (chain: A, length: 90)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1723 (1)	noe	96.7 (chain: A, length: 90)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	130 (130)	.	85.6 (chain: A, length: 90)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 98.9%
- Total number of assignments
  - ¹H chemical shifts: 511
  - ¹³C chemical shifts: 391
  - ¹⁵N chemical shifts: 90
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 96.7%
- Total number of restraints: 1718
- Weight of restraints: 1.0 (1718)
- Potential type of restraints: square-well-parabolic (1718)
- Range of distance target values: 2.02, 3.6 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 85.6%
- Total number of restraints: 130
- Total number of restraints per polymer type: 130
- Weight of restraints: 1.0 (130)
- Potential type of restraints: square-well-parabolic (130)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords E3 ligase, hoil-1, HOIP, ubiquitin, ubiquitin-like domain, UBLD