BMRB: 25601

Ensemble structure the closed state of Lys63-linked diubiquitin in the absence of a ligand

Authors

Liu, Z., Gong, Z.

Assembly

closed state of Lys63-linked diubiquitin

Entity

1. closed state of Lys63-linked diubiquitin, entity 1 (polymer), 76 monomers, 8528.742 Da Detail

MQIFVKTLTG KTITLEVEPS DTIECVKAKI QDKEGIPPDQ QRLIFAGCQL EDGRTLSDYN IQKESTLHLV LRLRGG

2. closed state of Lys63-linked diubiquitin, entity 2 (polymer), 71 monomers, 8025.098 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV L

3. closed state of Lys63-linked diubiquitin, entity MTN (non-polymer), 264.385 × 2 Da

Total weight

17082.61 Da

Max. entity weight

8528.742 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.5 %, Completeness: 29.7 %, Completeness (bb): 62.6 % Detail

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Polymer type: polypeptide(L)

	Total	1H	15N
All	29.7 % (319 of 1073)	20.1 % (184 of 917)	86.5 % (135 of 156)
Backbone	62.6 % (275 of 439)	47.0 % (140 of 298)	95.7 % (135 of 141)
Sidechain	6.9 % (44 of 634)	7.1 % (44 of 619)	0.0 % (0 of 15)
Aromatic	0.0 % (0 of 32)	0.0 % (0 of 32)
Methyl	12.5 % (12 of 96)	12.5 % (12 of 96)

1. entity 1

MQIFVKTLTG KTITLEVEPS DTIECVKAKI QDKEGIPPDQ QRLIFAGCQL EDGRTLSDYN IQKESTLHLV LRLRGG

2. entity 2

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV L

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 0.5mM 15N_proximal-14N_distalN25C_MTS protein were prepared for the intramolecular PRE measurement.

#	Name	Isotope labeling	Type	Concentration
1	N25C_MTS protein	[U-100% 15N]		0.5 mM
2	D2O	[U-99% 2H]		10 % v/v
3	sodium chloride	natural abundance		100 mM
4	sodium acetate	natural abundance		10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 0.5mM 15N_proximal-14N_distalK48C_MTS protein were prepared for the intramolecular PRE measurement.

#	Name	Isotope labeling	Type	Concentration
5	K48C_MTS protein	[U-100% 15N]		0.5 mM
6	D2O	[U-99% 2H]		10 % v/v
7	sodium chloride	natural abundance		100 mM
8	sodium acetate	natural abundance		10 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details A mixture of 0.5mM 15N_proximal-14N_distal and 0.5mM 14N_proximal-14N_distalN25C_MTS protein were prepared for the intermolecular PRE measurement.

#	Name	Isotope labeling	Type	Concentration
9	N25C_MTS mixture protein	[U-100% 15N]		1 mM
10	D2O	[U-99% 2H]		10 % v/v
11	sodium chloride	natural abundance		100 mM
12	sodium acetate	natural abundance		10 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details A mixture of 0.5mM 15N_proximal-14N_distal and 0.5mM 14N_proximal-14N_distalK48C_MTS protein were prepared for the intermolecular PRE measurement.

#	Name	Isotope labeling	Type	Concentration
13	K48C_MTS mixture protein	[U-100% 15N]		1 mM
14	D2O	[U-99% 2H]		10 % v/v
15	sodium chloride	natural abundance		100 mM
16	sodium acetate	natural abundance		10 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 15N_distal-14N_proximal

#	Name	Isotope labeling	Type	Concentration
17	15N_distal-14N_proximal	[U-100% 15N]		0.5 mM
18	D2O	[U-99% 2H]		10 % v/v
19	sodium chloride	natural abundance		100 mM
20	sodium acetate	natural abundance		10 mM

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 14N_distal-15N_proximal

#	Name	Isotope labeling	Type	Concentration
21	14N_distal-15N_proximal	[U-100% 15N]		0.5 mM
22	D2O	[U-99% 2H]		10 % v/v
23	sodium chloride	natural abundance		100 mM
24	sodium acetate	natural abundance		10 mM

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Calculated from 70 models in PDB: 2N2K, Strand ID: A, B Detail

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Release date

2015-07-12

Citation

Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition
Liu, Z., Gong, Z., Yang, J., Jiang, W., Zhu, W., Guo, D., Zhang, W., Liu, M., Tang, C.
Elife (2015), 4, e05767-e05767, PubMed 26090905 , DOI 10.7554/eLife.05767 , Abstract

Related entities 1. closed state of Lys63-linked diubiquitin, entity 1, : 1 : 236 : 190 entities Detail

Related entities 2. closed state of Lys63-linked diubiquitin, entity 2, : 204 : 10 : 77 : 308 entities Detail

Interaction partners 2. closed state of Lys63-linked diubiquitin, entity 2, : 27 interactors Detail

Experiments performed 6 experiments Detail