NMR solution structure of human ubiquitin-like domain of ubiquilin 1, Northeast Structural Genomics Consortium (NESG) target HT5A
MGSSHHHHHH SSGRENLYFQ GHPKIMKVTV KTPKEKEEFA VPENSSVQQF KEEISKRFKS HTDQLVLIFA GKILKDQDTL SQHGIHDGLT VHLVIKTQNR P
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 PSolvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Pressure 1.0 atm, Temperature 298 K, pH 7.0
Experiment name 2D 1H-15 HSQC (IPAP), 3D HNCO (IPAP)
List #1 RDC_list_1, RDC code DCCA, Field strength (1H) 600 MHz
List #1 RDC_list_1, RDC code DNH, Field strength (1H) 600 MHz
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
Bruker Avance - 800 MHz
State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | 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 % |
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
NoneOther bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
--------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
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MGSSHHHHHHSSGRENLYFQGHPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNR |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ......................PKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNR - P | P
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
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MGSSHHHHHHSSGRENLYFQGHPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNR |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ......................PKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNR - P | P
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MGSSHHHHHHSSGRENLYFQGHPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNR |||||||||| |||||||||| |||||||||||| |||||||||||||||| ||||| |||||||| || ......................PKIMKVTVKT..EKEEFAVPEN.SVQQFKEEISKR.KSHTDQLVLIFAGKIL...DTLSQ......LTVHLVIK..NR - P | P
RDC restraints
--------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