BMRBj - BMREntryMaster

Found 1 Document (0.699 seconds)

BMRB: 16390

2KLC

NMR solution structure of human ubiquitin-like domain of ubiquilin 1, Northeast Structural Genomics Consortium (NESG) target HT5A

Authors

Doherty, R.S., Dhe-Paganon, S., Fares, C., Lemak, S., Gutmanas, A., Garcia, M., Yee, A., Montelione, G.T., Arrowsmith, C.H.

Assembly

ubiquilin 1

Entity

1. ubiquilin 1 (polymer, Thiol state: not present), 101 monomers, 11597.99 Da Detail

MGSSHHHHHH SSGRENLYFQ GHPKIMKVTV KTPKEKEEFA VPENSSVQQF KEEISKRFKS HTDQLVLIFA GKILKDQDTL SQHGIHDGLT VHLVIKTQNR P

Formula weight

11597.99 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

restrained molecular dynamics

Data set

RDCs, assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 81.2 %, Completeness: 72.7 %, Completeness (bb): 76.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	72.7 % (886 of 1219)	73.6 % (471 of 640)	70.6 % (333 of 472)	76.6 % (82 of 107)
Backbone	76.1 % (455 of 598)	76.0 % (155 of 204)	76.1 % (226 of 297)	76.3 % (74 of 97)
Sidechain	70.7 % (506 of 716)	72.5 % (316 of 436)	67.4 % (182 of 270)	80.0 % (8 of 10)
Aromatic	21.6 % (22 of 102)	31.4 % (16 of 51)	11.8 % (6 of 51)
Methyl	91.7 % (88 of 96)	91.7 % (44 of 48)	91.7 % (44 of 48)

1. ubiquilin 1

MGSSHHHHHH SSGRENLYFQ GHPKIMKVTV KTPKEKEEFA VPENSSVQQF KEEISKRFKS HTDQLVLIFA GKILKDQDTL SQHGIHDGLT VHLVIKTQNR P

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.17 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.17 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 2.93 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

RDC

75 RDC values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1.0 atm, Temperature 298 K, pH 7.0 Detail

Release date

2009-07-06

Citation

Solution structure of ubiquitin-like domain of ubiquilin 1
Doherty, R.S., Dhe-Paganon, S., Fares, C., Lemak, S., Gutmanas, A., Garcia, M., Yee, A., Montelione, G.T., Arrowsmith, C.H.
Not known

Related entities 1. ubiquilin 1, : 1 : 25 entities Detail

Experiments performed 13 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

2 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

4 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

5 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

8 3D 1H-13C_arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

9 2D 1H-15 HSQC (IPAP)

Instrument

Bruker Avance - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

10 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

11 2D 1H-13C Constant Time HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

12 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

13 3D HNCO (IPAP)

Instrument

Bruker Avance - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	ubiquilin_1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride (NaCl)	natural abundance	300 mM
4	sodium azide (NaN3)	natural abundance	0.01 %
5	inhibitor cocktail (roche)	natural abundance	1 na
6	benzamidine	natural abundance	1 mM
7	ZnSO4	natural abundance	10 uM
8	DTT	natural abundance	10 mM
9	D20	natural abundance	10 %
10	H20	natural abundance	90 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16390_2klc.nef
Input source #2: Coordindates	2klc.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-------100
MGSSHHHHHHSSGRENLYFQGHPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGRENLYFQGHPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNR

-
P
|
P

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	101	0	0	100.0

Content subtype: combined_16390_2klc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	865		78.2 (chain: A, length: 101)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3000 (1)	noe	78.2 (chain: A, length: 101)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	24 (1)	hbond	13.9 (chain: A, length: 101)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_8	OK	84 (84)	.	63.4 (chain: A, length: 101)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	75 (75)	.	52.5 (chain: A, length: 101)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 78.2%
- Total number of assignments
  - ¹H chemical shifts: 458
  - ¹³C chemical shifts: 328
  - ¹⁵N chemical shifts: 79
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	640	458	71.6
¹³C chemical shifts	472	328	69.5
¹⁵N chemical shifts	110	79	71.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	204	151	74.0
¹³C chemical shifts	202	148	73.3
¹⁵N chemical shifts	97	71	73.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	436	307	70.4
¹³C chemical shifts	270	180	66.7
¹⁵N chemical shifts	13	8	61.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	43	86.0
¹³C chemical shifts	50	43	86.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	11	21.6
¹³C chemical shifts	51	6	11.8

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 78.2%
- Total number of restraints: 3000
- Weight of restraints: 1.0 (3000)
- Potential type of restraints: square-well-parabolic (3000)
- Range of distance target values: 2.25, 3.9 (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_2
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 13.9%
  - Total number of restraints: 24
  - Weight of restraints: 1.0 (24)
  - Potential type of restraints: square-well-parabolic (24)
  - Range of distance target values: 2.05, 3.0 (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_8
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 63.4%
- Total number of restraints: 84
- Total number of restraints per polymer type: 84
- Weight of restraints: 1.0 (84)
- Potential type of restraints: square-well-parabolic (84)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 52.5%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MGSSHHHHHHSSGRENLYFQGHPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNR
                      || |||||||    |  || ||     |||||||||||  ||| ||  |||||||||||||||||||| |||      
......................PK.MKVTVKT....E..AV.EN.....FKEEISKRFKS..DQL.LI..GKILKDQDTLSQHGIHDGLT.HLV      
--------10--------20--------30--------40--------50--------60--------70--------80--------90----      

-
P

Total number of restraints: 75
Potential type of restraints: undefined (75)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords Alzheimer's, NESG, Northeast Structural Genomics Consortium, OCSP, Ontario Centre for Structural Proteomics, PSI-2, Protein Structure Initiative, SGC, Structural Genomics, Structural Genomics Consortium, UBL, proteasome, protein binding, protein degradation, ubiquitin ligase-associated, ubiquitin-like, ubiquitination

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Found 1 Document (0.699 seconds)

BMRB: 16390

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ubiquilin 1, : 1 : 25 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 6 contents Detail