BMRBj - BMREntryMaster

Found 1 Document (2.857 seconds)

BMRB: 30675

4YC1

Solution-state NMR structural ensemble of human Tsg101 UEV in complex with K63-linked diubiquitin

Authors

Strickland, M., Watanabe, S., Bonn, S.M., Camara, C.M., Fushman, D., Carter, C.A., Tjandra, N.

Assembly

Ubiquitin, Tumor susceptibility gene 101 protein

Entity

1. Ubiquitin, Tumor susceptibility gene 101 protein, entity 1 (polymer, Thiol state: not present), 76 monomers, 8592.745 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQRESTLHLV LRLRGG

2. Ubiquitin, Tumor susceptibility gene 101 protein, entity 2 (polymer, Thiol state: not present), 77 monomers, 8679.818 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGD

3. Ubiquitin, Tumor susceptibility gene 101 protein, entity 3 (polymer, Thiol state: all free), 145 monomers, 16614.18 Da Detail

MAVSESQLKK MVSKYKYRDL TVRETVNVIT LYKDLKPVLD SYVFNDGSSR ELMNLTGTIP VPYRGNTYNI PICLWLLDTY PYNPPICFVK PTSSMTIKTG KHVDANGKIY LPYLHEWKHP QSDLLGLIQV MIVVFGDEPP VFSRP

Total weight

33886.742 Da

Max. entity weight

16614.18 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.3 %, Completeness: 25.3 %, Completeness (bb): 62.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	25.3 % (556 of 2196)	15.1 % (284 of 1875)	84.7 % (272 of 321)
Backbone	62.6 % (548 of 875)	46.3 % (276 of 596)	97.5 % (272 of 279)
Sidechain	0.6 % (8 of 1321)	0.6 % (8 of 1279)	0.0 % (0 of 42)
Aromatic	0.0 % (0 of 112)	0.0 % (0 of 110)	0.0 % (0 of 2)
Methyl	0.0 % (0 of 186)	0.0 % (0 of 186)

1. entity 1

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQRESTLHLV LRLRGG

2. entity 2

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGD

3. entity 3

MAVSESQLKK MVSKYKYRDL TVRETVNVIT LYKDLKPVLD SYVFNDGSSR ELMNLTGTIP VPYRGNTYNI PICLWLLDTY PYNPPICFVK PTSSMTIKTG KHVDANGKIY LPYLHEWKHP QSDLLGLIQV MIVVFGDEPP VFSRP

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM [U-98% 15N] Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Tsg101 UEV domain	[U-98% 15N]	200 uM
2	K63-linked diubiquitin, distal domain	natural abundance	200 uM
3	K63-linked diubiquitin, proximal domain	natural abundance	200 uM
4	potassium phosphate	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM Tsg101 UEV domain, 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
6	Tsg101 UEV domain	natural abundance	200 uM
7	K63-linked diubiquitin, distal domain	[U-98% 15N]	200 uM
8	K63-linked diubiquitin, proximal domain	natural abundance	200 uM
9	potassium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM

Sample #3

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
11	Tsg101 UEV domain	natural abundance	200 uM
12	K63-linked diubiquitin, distal domain	natural abundance	200 uM
13	K63-linked diubiquitin, proximal domain	[U-98% 15N]	200 uM
14	potassium phosphate	natural abundance	20 mM
15	sodium chloride	natural abundance	50 mM

Sample #4

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
16	Tsg101 UEV domain	[U-98% 15N]	125 uM
17	K63-linked diubiquitin, distal domain	natural abundance	125 uM
18	K63-linked diubiquitin, proximal domain	natural abundance	125 uM
19	potassium phosphate	natural abundance	20 mM
20	sodium chloride	natural abundance	50 mM

Sample #5

#	Name	Isotope labeling	Concentration
21	Tsg101 UEV domain	[U-98% 15N]	125 uM
22	K63-linked diubiquitin, distal domain	natural abundance	125 uM
23	K63-linked diubiquitin, proximal domain	natural abundance	125 uM
24	potassium phosphate	natural abundance	20 mM
25	sodium chloride	natural abundance	50 mM

Sample #6

#	Name	Isotope labeling	Concentration
26	Tsg101 UEV domain	[U-98% 15N]	125 uM
27	K63-linked diubiquitin, distal domain	natural abundance	125 uM
28	K63-linked diubiquitin, proximal domain	natural abundance	125 uM
29	potassium phosphate	natural abundance	20 mM
30	sodium chloride	natural abundance	50 mM

Sample #7

#	Name	Isotope labeling	Concentration
31	Tsg101 UEV domain	[U-98% 15N]	125 uM
32	K63-linked diubiquitin, distal domain	natural abundance	125 uM
33	K63-linked diubiquitin, proximal domain	natural abundance	125 uM
34	potassium phosphate	natural abundance	20 mM
35	sodium chloride	natural abundance	50 mM

Sample #8

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM [U-98% 15N] Tsg101 UEV domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
36	Tsg101 UEV domain	[U-98% 15N]	200 uM
37	potassium phosphate	natural abundance	20 mM
38	sodium chloride	natural abundance	50 mM

Sample #9

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
39	K63-linked diubiquitin, distal domain	[U-98% 15N]	200 uM
40	K63-linked diubiquitin, proximal domain	natural abundance	200 uM
41	potassium phosphate	natural abundance	20 mM
42	sodium chloride	natural abundance	50 mM

Sample #10

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
43	K63-linked diubiquitin, distal domain	natural abundance	200 uM
44	K63-linked diubiquitin, proximal domain	[U-98% 15N]	200 uM
45	potassium phosphate	natural abundance	20 mM
46	sodium chloride	natural abundance	50 mM

Release date

2019-10-01

Citation

Dual Binding Modes of K63-Linked Diubiquitin Regulate Tsg101/ESCRT-I Recruitment
Strickland, M., Watanabe, S., Bonn, S.M., Camara, C.M., Fushman, D., Carter, C.A., Tjandra, N.

Related entities 1. Ubiquitin, Tumor susceptibility gene 101 protein, entity 1, : 98 : 229 entities Detail

Related entities 2. Ubiquitin, Tumor susceptibility gene 101 protein, entity 2, : 134 : 193 entities Detail

Related entities 3. Ubiquitin, Tumor susceptibility gene 101 protein, entity 3, : 1 : 11 : 3 : 40 entities Detail

Interaction partners 3. Ubiquitin, Tumor susceptibility gene 101 protein, entity 3, : 109 interactors Detail

More details for 109 interactors identified by 28 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 800 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM [U-98% 15N] Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Tsg101 UEV domain	[U-98% 15N]	200 uM
2	K63-linked diubiquitin, distal domain	natural abundance	200 uM
3	K63-linked diubiquitin, proximal domain	natural abundance	200 uM
4	potassium phosphate	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM

2 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM Tsg101 UEV domain, 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
6	Tsg101 UEV domain	natural abundance	200 uM
7	K63-linked diubiquitin, distal domain	[U-98% 15N]	200 uM
8	K63-linked diubiquitin, proximal domain	natural abundance	200 uM
9	potassium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM

3 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
11	Tsg101 UEV domain	natural abundance	200 uM
12	K63-linked diubiquitin, distal domain	natural abundance	200 uM
13	K63-linked diubiquitin, proximal domain	[U-98% 15N]	200 uM
14	potassium phosphate	natural abundance	20 mM
15	sodium chloride	natural abundance	50 mM

4 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
16	Tsg101 UEV domain	[U-98% 15N]	125 uM
17	K63-linked diubiquitin, distal domain	natural abundance	125 uM
18	K63-linked diubiquitin, proximal domain	natural abundance	125 uM
19	potassium phosphate	natural abundance	20 mM
20	sodium chloride	natural abundance	50 mM

5 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 600 MHz Cryoprobe

Sample

State anisotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
21	Tsg101 UEV domain	[U-98% 15N]	125 uM
22	K63-linked diubiquitin, distal domain	natural abundance	125 uM
23	K63-linked diubiquitin, proximal domain	natural abundance	125 uM
24	potassium phosphate	natural abundance	20 mM
25	sodium chloride	natural abundance	50 mM

6 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 600 MHz Cryoprobe

Sample

#	Name	Isotope labeling	Concentration
26	Tsg101 UEV domain	[U-98% 15N]	125 uM
27	K63-linked diubiquitin, distal domain	natural abundance	125 uM
28	K63-linked diubiquitin, proximal domain	natural abundance	125 uM
29	potassium phosphate	natural abundance	20 mM
30	sodium chloride	natural abundance	50 mM

7 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 600 MHz Cryoprobe

Sample

#	Name	Isotope labeling	Concentration
31	Tsg101 UEV domain	[U-98% 15N]	125 uM
32	K63-linked diubiquitin, distal domain	natural abundance	125 uM
33	K63-linked diubiquitin, proximal domain	natural abundance	125 uM
34	potassium phosphate	natural abundance	20 mM
35	sodium chloride	natural abundance	50 mM

8 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 800 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM [U-98% 15N] Tsg101 UEV domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
36	Tsg101 UEV domain	[U-98% 15N]	200 uM
37	potassium phosphate	natural abundance	20 mM
38	sodium chloride	natural abundance	50 mM

9 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
39	K63-linked diubiquitin, distal domain	[U-98% 15N]	200 uM
40	K63-linked diubiquitin, proximal domain	natural abundance	200 uM
41	potassium phosphate	natural abundance	20 mM
42	sodium chloride	natural abundance	50 mM

10 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8, Details 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
43	K63-linked diubiquitin, distal domain	natural abundance	200 uM
44	K63-linked diubiquitin, proximal domain	[U-98% 15N]	200 uM
45	potassium phosphate	natural abundance	20 mM
46	sodium chloride	natural abundance	50 mM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30675_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	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30675_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	542		93.4 (chain: 1, length: 76), 93.5 (chain: 2, length: 77), 88.3 (chain: 3, length: 145)
1	Chemical shift references	chem_shift_reference_1	OK	2		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 76, Sequence coverage: 93.4%
  - Entity_assembly_ID: 2, Chain length: 77, Sequence coverage: 93.5%
  - Entity_assembly_ID: 3, Chain length: 145, Sequence coverage: 88.3%
- Total number of assignments
  - ¹H chemical shifts: 271
  - ¹⁵N chemical shifts: 271
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
  - Entity_assemble_ID: 3
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1
  - Chain_ID: 2
  - Chain_ID: 3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	477	71	14.9
¹⁵N chemical shifts	86	71	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	155	71	45.8
¹⁵N chemical shifts	73	71	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	322	0	0.0
¹⁵N chemical shifts	13	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	482	72	14.9
¹⁵N chemical shifts	86	72	83.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	157	72	45.9
¹⁵N chemical shifts	74	72	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	325	0	0.0
¹⁵N chemical shifts	12	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	916	128	14.0
¹⁵N chemical shifts	149	128	85.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	284	128	45.1
¹⁵N chemical shifts	132	128	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	632	0	0.0
¹⁵N chemical shifts	17	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	93	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	0	0.0
¹⁵N chemical shifts	2	0	0.0

Keywords ESCRT-I, cell cycle, ubiquitin E2 variant, viral budding

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (2.857 seconds)

BMRB: 30675

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Sample #7

Sample #8

Sample #9

Sample #10

Related entities 1. Ubiquitin, Tumor susceptibility gene 101 protein, entity 1, : 98 : 229 entities Detail

Related entities 2. Ubiquitin, Tumor susceptibility gene 101 protein, entity 2, : 134 : 193 entities Detail

Related entities 3. Ubiquitin, Tumor susceptibility gene 101 protein, entity 3, : 1 : 11 : 3 : 40 entities Detail

Interaction partners 3. Ubiquitin, Tumor susceptibility gene 101 protein, entity 3, : 109 interactors Detail

Experiments performed 10 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 5 contents Detail