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BMRB: 36081

5XK4

Retracted state of S65-phosphorylated ubiquitin

Authors

Dong, X., Gong, Z., Qin, L.Y., Ran, M.L., Zhang, C.L., Liu, K., Liu, Z., Zhang, W.P., Tang, C.

Assembly

retracted phosphorylated ubiquitin

Entity

1. retracted phosphorylated ubiquitin (polymer, Thiol state: not present), 76 monomers, 8644.710 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKEXTLHLV LRLRGG

Formula weight

8644.71 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.7 %, Completeness: 74.3 %, Completeness (bb): 90.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.3 % (669 of 901)	67.9 % (322 of 474)	81.6 % (283 of 347)	80.0 % (64 of 80)
Backbone	90.5 % (402 of 444)	89.5 % (137 of 153)	91.8 % (201 of 219)	88.9 % (64 of 72)
Sidechain	63.3 % (333 of 526)	57.6 % (185 of 321)	75.1 % (148 of 197)	0.0 % (0 of 8)
Aromatic	18.8 % (6 of 32)	37.5 % (6 of 16)	0.0 % (0 of 16)
Methyl	82.7 % (81 of 98)	77.6 % (38 of 49)	87.8 % (43 of 49)

1. Polyubiquitin-B

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKEXTLHLV LRLRGG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	phosphorylated ubiquitin	[U-98% 13C; U-98% 15N]	protein	0.8 mM
2	HEPES	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	150 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

LACS Plot; CA

Referencing offset: -0.26 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.26 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.29 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 30 models in PDB: 5XK4, Strand ID: A Detail

Release date

2017-08-01

Citation

Ubiquitin S65 phosphorylation engenders a pH-sensitive conformational switch
Dong, X., Gong, Z., Lu, Y.B., Liu, K., Qin, L.Y., Ran, M.L., Zhang, C.L., Liu, Z., Zhang, W.P., Tang, C.
Proc. Natl. Acad. Sci. U. S. A. (2017), 114, 6770-6775, PubMed 28611216 , DOI 10.1073/pnas.1705718114 , Abstract

Related entities 1. retracted phosphorylated ubiquitin, : 384 : 340 entities Detail

Interaction partners 1. retracted phosphorylated ubiquitin, : 27 interactors Detail

More details for 27 interactors identified by 16 citations

Experiments performed 6 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	phosphorylated ubiquitin	[U-98% 13C; U-98% 15N]	protein	0.8 mM
2	HEPES	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	150 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

2 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	phosphorylated ubiquitin	[U-98% 13C; U-98% 15N]	protein	0.8 mM
2	HEPES	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	150 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

3 3D HNCA

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	phosphorylated ubiquitin	[U-98% 13C; U-98% 15N]	protein	0.8 mM
2	HEPES	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	150 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

4 3D HNCACB

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	phosphorylated ubiquitin	[U-98% 13C; U-98% 15N]	protein	0.8 mM
2	HEPES	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	150 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

5 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	phosphorylated ubiquitin	[U-98% 13C; U-98% 15N]	protein	0.8 mM
2	HEPES	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	150 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

6 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	phosphorylated ubiquitin	[U-98% 13C; U-98% 15N]	protein	0.8 mM
2	HEPES	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	150 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

nullKeywords CELL CYCLE, pH-sensitive ubiquitin conformational switch