BMRBj - BMREntryMaster

Found 1 Document (0.667 seconds)

BMRB: 27977

Solution structure of the PUB domain of human UBXD1 protein

Authors

Beuck, C., Bayer, P., Blueggel, M.

Assembly

UBXD1-PUB domain

Entity

1. UBXD1-PUB domain (polymer, Thiol state: all free), 119 monomers, 13803.41 Da Detail

GSHMSTDPVA ASIMKIYTFN KDQDRVKLGV DTIAKYLDNI HLHPEEEKYR KIKLQNKVFQ ERINCLEGTH EFFEAIGFQK VLLPAQDQED PEEFYVLSET TLAQPQSLER HKEQLLAAE

Formula weight

13803.41 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.5 %, Completeness: 92.6 %, Completeness (bb): 95.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.6 % (1336 of 1442)	90.6 % (685 of 756)	96.1 % (537 of 559)	89.8 % (114 of 127)
Backbone	95.6 % (673 of 704)	94.9 % (225 of 237)	96.3 % (340 of 353)	94.7 % (108 of 114)
Sidechain	90.9 % (775 of 853)	88.6 % (460 of 519)	96.3 % (309 of 321)	46.2 % (6 of 13)
Aromatic	89.3 % (100 of 112)	91.1 % (51 of 56)	87.5 % (49 of 56)
Methyl	96.9 % (124 of 128)	93.8 % (60 of 64)	100.0 % (64 of 64)

1. UBXD1-PUB domain

GSHMSTDPVA ASIMKIYTFN KDQDRVKLGV DTIAKYLDNI HLHPEEEKYR KIKLQNKVFQ ERINCLEGTH EFFEAIGFQK VLLPAQDQED PEEFYVLSET TLAQPQSLER HKEQLLAAE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 13C,15N-labeled in D2O

#	Name	Isotope labeling	Type	Concentration
7	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		500 uM
8	potassium phosphate	natural abundance		16 mM
9	sodium phosphate	natural abundance		34 mM
10	D2O	[U-99% 2H]		100 %
11	DSS	natural abundance		0.1 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N-labeled in water

#	Name	Isotope labeling	Type	Concentration
12	UBXD1-PUB domain	[U-98% 15N]		700 uM
13	potassium phosphate	natural abundance		16 mM
14	sodium phosphate	natural abundance		34 mM
15	H2O	natural abundance		90 %
16	D2O	[U-2H]		10 %
17	DSS	natural abundance		0.1 mM

LACS Plot; CA

Referencing offset: -0.06 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.06 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: 0.1 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.14 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6SAP, Strand ID: A Detail

Release date

2019-07-17

Citation

Structure of the PUB Domain from Ubiquitin Regulatory X Domain Protein 1 (UBXD1) and Its Interaction with the p97 AAA+ ATPase
Blueggel, M., van den Boom, J., Meyer, H., Bayer, P., Beuck, C.
Biomolecules (2019), 9, 876-876, PubMed 31847414 , DOI 10.3390/biom9120876 , Abstract

Related entities 1. UBXD1-PUB domain, : 2 : 8 entities Detail

Interaction partners 1. UBXD1-PUB domain, : 10 interactors Detail

More details for 10 interactors identified by 6 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 13C,15N-labeled in D2O

#	Name	Isotope labeling	Type	Concentration
7	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		500 uM
8	potassium phosphate	natural abundance		16 mM
9	sodium phosphate	natural abundance		34 mM
10	D2O	[U-99% 2H]		100 %
11	DSS	natural abundance		0.1 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

4 3D HNCACB

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

5 3D HNCO

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

6 3D HN(CA)CO

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

7 3D H(CCO)NH

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

8 3D (H)C(CO)NH

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

9 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N-labeled in water

#	Name	Isotope labeling	Type	Concentration
12	UBXD1-PUB domain	[U-98% 15N]		700 uM
13	potassium phosphate	natural abundance		16 mM
14	sodium phosphate	natural abundance		34 mM
15	H2O	natural abundance		90 %
16	D2O	[U-2H]		10 %
17	DSS	natural abundance		0.1 mM

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N-labeled in water

#	Name	Isotope labeling	Type	Concentration
12	UBXD1-PUB domain	[U-98% 15N]		700 uM
13	potassium phosphate	natural abundance		16 mM
14	sodium phosphate	natural abundance		34 mM
15	H2O	natural abundance		90 %
16	D2O	[U-2H]		10 %
17	DSS	natural abundance		0.1 mM

11 3D HC(C)H-COSY aliphatic

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 13C,15N-labeled in D2O

#	Name	Isotope labeling	Type	Concentration
7	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		500 uM
8	potassium phosphate	natural abundance		16 mM
9	sodium phosphate	natural abundance		34 mM
10	D2O	[U-99% 2H]		100 %
11	DSS	natural abundance		0.1 mM

12 3D HC(C)H-TOCSY aliphatic

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 13C,15N-labeled in D2O

#	Name	Isotope labeling	Type	Concentration
7	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		500 uM
8	potassium phosphate	natural abundance		16 mM
9	sodium phosphate	natural abundance		34 mM
10	D2O	[U-99% 2H]		100 %
11	DSS	natural abundance		0.1 mM

13 3D HC(C)H-TOCSY

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

14 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

15 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

16 2D Histidin H(C)N-SOFAST-HMQC

Instrument

Bruker Avance - 700 MHz inverse TCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 15N,13C-labeled in water

#	Name	Isotope labeling	Type	Concentration
1	UBXD1-PUB domain	[U-98% 13C; U-98% 15N]		600-900 uM
2	potassium phosphate	natural abundance		16 mM
3	sodium phosphate	natural abundance		34 mM
4	H2O	natural abundance		90 %
5	D2O	[U-2H]		10 %
6	DSS	natural abundance		0.1 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr27977_3.str
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

Content subtype: bmr27977_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1463		96.6 (chain: 1, length: 119)
1	Chemical shift references	chemical_shift_reference_1	OK	2		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 119, Sequence coverage: 96.6%
- Total number of assignments
  - ¹H chemical shifts: 811
  - ¹³C chemical shifts: 535
  - ¹⁵N chemical shifts: 117
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- 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: 1

Keywords NMR solution structure, PUB domain, UBXD1, p97, protein interaction