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BMRB: 18669

2LXA

Solution structure of the Get5 ubiquitin-like domain

Authors

Chartron, J.W., VanderVelde, D.G., Clemons, W.M.

Assembly

Get5

Entity

1. Get5 (polymer, Thiol state: not present), 87 monomers, 9978.505 Da Detail

MVHLTLKKIQ APKFSIEHDF SPSDTILQIK QHLISEEKAS HISEIKLLLK GKVLHDNLFL SDLKVTPANS TITVMIKPNL EHHHHHH

Formula weight

9978.505 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.0 %, Completeness: 75.4 %, Completeness (bb): 76.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.4 % (804 of 1066)	79.6 % (441 of 554)	67.4 % (285 of 423)	87.6 % (78 of 89)
Backbone	76.3 % (392 of 514)	86.0 % (147 of 171)	66.5 % (173 of 260)	86.7 % (72 of 83)
Sidechain	76.8 % (490 of 638)	76.8 % (294 of 383)	76.3 % (190 of 249)	100.0 % (6 of 6)
Aromatic	16.2 % (12 of 74)	32.4 % (12 of 37)	0.0 % (0 of 37)
Methyl	96.6 % (112 of 116)	96.6 % (56 of 58)	96.6 % (56 of 58)

1. Get5

MVHLTLKKIQ APKFSIEHDF SPSDTILQIK QHLISEEKAS HISEIKLLLK GKVLHDNLFL SDLKVTPANS TITVMIKPNL EHHHHHH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297.5 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
1	Get5	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		0.02 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.09 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2LXA, Strand ID: A Detail

Release date

2012-11-19

Citation

Structures of the Sgt2/SGTA dimerization domain with the Get5/UBL4A UBL domain reveal an interaction that forms a conserved dynamic interface
Chartron, J.W., VanderVelde, D.G., Clemons, W.M.
Cell Rep. (2012), 2, 1620-1632, PubMed 23142665 , DOI 10.1016/j.celrep.2012.10.010 , Abstract

Related entities 1. Get5, : 1 : 7 : 55 entities Detail

Interaction partners 1. Get5, : 15 interactors Detail

More details for 15 interactors identified by 5 citations

Experiments performed 7 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 297.5 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
1	Get5	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		0.02 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297.5 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
1	Get5	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		0.02 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297.5 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
1	Get5	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		0.02 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D (H)CCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297.5 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
1	Get5	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		0.02 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297.5 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
1	Get5	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		0.02 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297.5 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
1	Get5	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		0.02 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297.5 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
1	Get5	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		0.02 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18669_2lxa.nef
Input source #2: Coordindates	2lxa.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

------80--------90-------100-------110-------120-------130-------140-------150---------
MVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPNLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPNLEHHHHHH
--------10--------20--------30--------40--------50--------60--------70--------80-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	87	0	0	100.0

Content subtype: combined_18669_2lxa.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	786		92.0 (chain: A, length: 87)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2208 (1)	noe	90.8 (chain: A, length: 87)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	52 (1)	hbond	39.1 (chain: A, length: 87)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	124 (124)	.	83.9 (chain: A, length: 87)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 92.0%
- Total number of assignments
  - ¹H chemical shifts: 438
  - ¹³C chemical shifts: 270
  - ¹⁵N chemical shifts: 78
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 90.8%
- Total number of restraints: 2208
- Weight of restraints: 1.0 (2208)
- Potential type of restraints: square-well-parabolic (2208)
- Range of distance target values: 1.68, 5.36 (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: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 39.1%
  - Total number of restraints: 52
  - Weight of restraints: 1.0 (52)
  - Potential type of restraints: square-well-parabolic (52)
  - Range of distance target values: 2.05, 3.05 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 83.9%
- Total number of restraints: 124
- Total number of restraints per polymer type: 124
- Weight of restraints: 1.0 (124)
- Potential type of restraints: square-well-parabolic (124)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords GET pathway, protein-protein interaction, Sgt2 binding domain, ubiquitin-like domain