BMRBj - BMREntryMaster

Found 1 Document (7.428 seconds)

BMRB: 30602

6OQ2

NMR Structure of Branched K11/K48-Linked Tri-Ubiquitin

Authors

Boughton, A.J., Fushman, D.

Assembly

Branched K11/K48-Linked Tri-Ubiquitin

Entity

1. Branched K11/K48-Linked Tri-Ubiquitin, entity 1 (polymer, Thiol state: not present), 76 monomers, 8648.773 Da Detail

MQIFVKTLTG RTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGRQL EDGRTLSDYN IQRESTLHLV LRLRGG

2. Branched K11/K48-Linked Tri-Ubiquitin, entity 2 (polymer, Thiol state: not present), 76 monomers, 8592.745 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGRQL EDGRTLSDYN IQKESTLHLV LRLRGG

3. Branched K11/K48-Linked Tri-Ubiquitin, entity 3 (polymer, Thiol state: not present), 77 monomers, 8679.818 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGD

Total weight

25921.338 Da

Max. entity weight

8679.818 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 34.1 %, Completeness: 10.7 %, Completeness (bb): 22.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	10.7 % (179 of 1678)	7.5 % (107 of 1434)	29.5 % (72 of 244)
Backbone	22.6 % (155 of 687)	17.8 % (83 of 467)	32.7 % (72 of 220)
Sidechain	2.4 % (24 of 991)	2.5 % (24 of 967)	0.0 % (0 of 24)
Aromatic	0.0 % (0 of 48)	0.0 % (0 of 48)
Methyl	4.8 % (7 of 147)	4.8 % (7 of 147)

1. entity 1

MQIFVKTLTG RTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGRQL EDGRTLSDYN IQRESTLHLV LRLRGG

2. entity 2

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGRQL EDGRTLSDYN IQKESTLHLV LRLRGG

3. entity 3

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGD

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 120 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	[U-15N-distal11]	120 uM
2	entity_2	[U-15N-distal11]	120 uM
3	entity_3	[U-15N-distal11]	120 uM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	entity_1	[U-15N-distal48]	100 uM
5	entity_2	[U-15N-distal48]	100 uM
6	entity_3	[U-15N-distal48]	100 uM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 60 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	entity_1	[U-15N-distal11]	60 uM
8	entity_2	[U-15N-distal11]	60 uM
9	entity_3	[U-15N-distal11]	60 uM

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 110 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
10	entity_1	[U-15N-distal48]	110 uM
11	entity_2	[U-15N-distal48]	110 uM
12	entity_3	[U-15N-distal48]	110 uM

Chem. Shift Complete2

Sequence coverage: 34.5 %, Completeness: 10.8 %, Completeness (bb): 23.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	10.8 % (362 of 3356)	7.4 % (212 of 2868)	30.7 % (150 of 488)
Backbone	23.1 % (318 of 1374)	18.1 % (169 of 934)	33.9 % (149 of 440)
Sidechain	2.2 % (44 of 1982)	2.2 % (43 of 1934)	2.1 % (1 of 48)
Aromatic	0.0 % (0 of 96)	0.0 % (0 of 96)
Methyl	4.1 % (12 of 294)	4.1 % (12 of 294)

1. entity 1

MQIFVKTLTG RTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGRQL EDGRTLSDYN IQRESTLHLV LRLRGG

2. entity 2

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGRQL EDGRTLSDYN IQKESTLHLV LRLRGG

3. entity 3

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGD

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 120 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	[U-15N-distal11]	120 uM
2	entity_2	[U-15N-distal11]	120 uM
3	entity_3	[U-15N-distal11]	120 uM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	entity_1	[U-15N-distal48]	100 uM
5	entity_2	[U-15N-distal48]	100 uM
6	entity_3	[U-15N-distal48]	100 uM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 60 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	entity_1	[U-15N-distal11]	60 uM
8	entity_2	[U-15N-distal11]	60 uM
9	entity_3	[U-15N-distal11]	60 uM

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 110 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
10	entity_1	[U-15N-distal48]	110 uM
11	entity_2	[U-15N-distal48]	110 uM
12	entity_3	[U-15N-distal48]	110 uM

Protein Blocks Logo

Calculated from 10 models in PDB: 6OQ2, Strand ID: B, D, E Detail

Release date

2019-04-29

Citation

Branching via K11 and K48 Bestows Ubiquitin Chains with a Unique Interdomain Interface and Enhanced Affinity for Proteasomal Subunit Rpn1
Boughton, A.J., Krueger, S., Fushman, D.
Structure (2020), 28, 29-43, PubMed 31677892 , DOI 10.1016/j.str.2019.10.008 , Abstract

Related entities 1. Branched K11/K48-Linked Tri-Ubiquitin, entity 1, : 2 : 311 : 1 : 409 entities Detail

Related entities 2. Branched K11/K48-Linked Tri-Ubiquitin, entity 2, : 1 : 13 : 300 : 409 entities Detail

Related entities 3. Branched K11/K48-Linked Tri-Ubiquitin, entity 3, : 1 : 21 : 340 : 340 entities Detail

Interaction partners 1. Branched K11/K48-Linked Tri-Ubiquitin, entity 1, : 27 interactors Detail

More details for 27 interactors identified by 16 citations

Interaction partners 2. Branched K11/K48-Linked Tri-Ubiquitin, entity 2, : 27 interactors Detail

More details for 27 interactors identified by 16 citations

Interaction partners 3. Branched K11/K48-Linked Tri-Ubiquitin, entity 3, : 27 interactors Detail

More details for 27 interactors identified by 16 citations

Experiments performed 4 experiments Detail

Chemical shift validation 6 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30602_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	Warning

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr30602_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	140	92.1 (chain: 1, length: 76)
2	Assigned chemical shifts	assigned_chemical_shifts_2	Warning	140	92.1 (chain: 2, length: 76)
1	Chemical shift references	chem_shift_reference_1	OK	2	No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 76, Sequence coverage: 92.1%
- Total number of assignments
  - ¹H chemical shifts: 70
  - ¹⁵N chemical shifts: 70
- Completeness of assignments
  - Entity_assemble_ID: 1
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1
Saveframe: assigned_chemical_shifts_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 76, Sequence coverage: 92.1%
- Total number of assignments
  - ¹H chemical shifts: 70
  - ¹⁵N chemical shifts: 70
- Completeness of assignments
  - Entity_assemble_ID: 2
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	475	70	14.7
¹⁵N chemical shifts	88	70	79.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	155	70	45.2
¹⁵N chemical shifts	73	70	95.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	320	0	0.0
¹⁵N chemical shifts	15	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	477	70	14.7
¹⁵N chemical shifts	86	70	81.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	155	70	45.2
¹⁵N chemical shifts	73	70	95.9

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

Keywords SIGNALING PROTEIN

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Found 1 Document (7.428 seconds)

BMRB: 30602

Sample #1

Sample #2

Sample #3

Sample #4

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. Branched K11/K48-Linked Tri-Ubiquitin, entity 1, : 2 : 311 : 1 : 409 entities Detail

Related entities 2. Branched K11/K48-Linked Tri-Ubiquitin, entity 2, : 1 : 13 : 300 : 409 entities Detail

Related entities 3. Branched K11/K48-Linked Tri-Ubiquitin, entity 3, : 1 : 21 : 340 : 340 entities Detail

Interaction partners 1. Branched K11/K48-Linked Tri-Ubiquitin, entity 1, : 27 interactors Detail

Interaction partners 2. Branched K11/K48-Linked Tri-Ubiquitin, entity 2, : 27 interactors Detail

Interaction partners 3. Branched K11/K48-Linked Tri-Ubiquitin, entity 3, : 27 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 6 contents Detail