BMRBj - BMREntryMaster

Found 1 Document (0.801 seconds)

BMRB: 28042

ubiquitin receptor protein complex

Authors

Lu, X., Walters, K.J.

Assembly

ubiquitin receptor

Entity

1. ubiquitin receptor A (polymer, Thiol state: all free), 136 monomers, 15393.35 Da Detail

GPGSMTTSGA LFPSLVPGSR GASNKYLVEF RAGKMSLKGT TVTPDKRKGL VYIQQTDDSL IHFCWKDRTS GNVEDDLIIF PDDCEFKRVP QCPSGRVYVL KFKAGSKRLF FWMQEPKTDQ DEEHCRKVNE YLNNPP

2. ubiquitin receptor B (polymer, Thiol state: all free), 36 monomers, 3626.821 Da Detail

MPGALGASGS SGHELSALGP GSQEPEPPEP FEYIDD

3. ubiquitin receptor C (polymer, Thiol state: all free), 77 monomers, 8679.818 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGD

4. ubiquitin receptor D (polymer, Thiol state: all free), 76 monomers, 8592.745 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGRQL EDGRTLSDYN IQKESTLHLV LRLRGG

Total weight

36292.734 Da

Max. entity weight

15393.35 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 45.5 %, Completeness: 41.5 %, Completeness (bb): 40.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	41.5 % (1577 of 3803)	42.3 % (846 of 1999)	40.9 % (602 of 1472)	38.9 % (129 of 332)
Backbone	40.7 % (775 of 1906)	40.5 % (266 of 657)	41.4 % (392 of 946)	38.6 % (117 of 303)
Sidechain	42.3 % (927 of 2193)	43.2 % (580 of 1342)	40.8 % (335 of 822)	41.4 % (12 of 29)
Aromatic	53.5 % (123 of 230)	65.2 % (75 of 115)	40.7 % (46 of 113)	100.0 % (2 of 2)
Methyl	38.3 % (128 of 334)	38.3 % (64 of 167)	38.3 % (64 of 167)

1. ubiquitin receptor A

GPGSMTTSGA LFPSLVPGSR GASNKYLVEF RAGKMSLKGT TVTPDKRKGL VYIQQTDDSL IHFCWKDRTS GNVEDDLIIF PDDCEFKRVP QCPSGRVYVL KFKAGSKRLF FWMQEPKTDQ DEEHCRKVNE YLNNPP

2. ubiquitin receptor B

MPGALGASGS SGHELSALGP GSQEPEPPEP FEYIDD

3. ubiquitin receptor C

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGD

4. ubiquitin receptor D

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGRQL EDGRTLSDYN IQKESTLHLV LRLRGG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Rpn13	[U-13C]	0.6 mM
2	Rpn2	natural abundance	0.6 mM
3	proximal ubiquitin of Diubiquitin	[U-13C]	0.72 mM
4	proximal ubiquitin of Diubiquitin	[U-13C]	0.72 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	Rpn13	[U-13C]	0.6 mM
6	Rpn2	natural abundance	0.6 mM
7	distal ubiquitin of Diubiquitin	[U-13C]	0.72 mM
8	distal ubiquitin of Diubiquitin	[U-13C]	0.72 mM

Chem. Shift Complete2

Sequence coverage: 25.5 %, Completeness: 28.8 %, Completeness (bb): 30.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	28.8 % (2189 of 7606)	29.0 % (1161 of 3998)	28.2 % (829 of 2944)	30.0 % (199 of 664)
Backbone	30.4 % (1157 of 3812)	30.6 % (402 of 1314)	30.1 % (570 of 1892)	30.5 % (185 of 606)
Sidechain	27.8 % (1219 of 4386)	28.3 % (759 of 2684)	27.1 % (445 of 1644)	25.9 % (15 of 58)
Aromatic	31.7 % (146 of 460)	38.3 % (88 of 230)	24.8 % (56 of 226)	50.0 % (2 of 4)
Methyl	23.7 % (158 of 668)	24.3 % (81 of 334)	23.1 % (77 of 334)

1. ubiquitin receptor A

GPGSMTTSGA LFPSLVPGSR GASNKYLVEF RAGKMSLKGT TVTPDKRKGL VYIQQTDDSL IHFCWKDRTS GNVEDDLIIF PDDCEFKRVP QCPSGRVYVL KFKAGSKRLF FWMQEPKTDQ DEEHCRKVNE YLNNPP

2. ubiquitin receptor B

MPGALGASGS SGHELSALGP GSQEPEPPEP FEYIDD

3. ubiquitin receptor C

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGD

4. ubiquitin receptor D

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGRQL EDGRTLSDYN IQKESTLHLV LRLRGG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Rpn13	[U-13C]	0.6 mM
2	Rpn2	natural abundance	0.6 mM
3	proximal ubiquitin of Diubiquitin	[U-13C]	0.72 mM
4	proximal ubiquitin of Diubiquitin	[U-13C]	0.72 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	Rpn13	[U-13C]	0.6 mM
6	Rpn2	natural abundance	0.6 mM
7	distal ubiquitin of Diubiquitin	[U-13C]	0.72 mM
8	distal ubiquitin of Diubiquitin	[U-13C]	0.72 mM

Chem. Shift Complete3

Sequence coverage: 35.7 %, Completeness: 29.3 %, Completeness (bb): 30.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	29.3 % (3341 of 11409)	29.6 % (1778 of 5997)	28.9 % (1276 of 4416)	28.8 % (287 of 996)
Backbone	30.1 % (1720 of 5718)	30.6 % (603 of 1971)	30.1 % (853 of 2838)	29.0 % (264 of 909)
Sidechain	29.0 % (1908 of 6579)	29.2 % (1177 of 4026)	28.7 % (707 of 2466)	27.6 % (24 of 87)
Aromatic	25.2 % (174 of 690)	29.6 % (102 of 345)	20.6 % (70 of 339)	33.3 % (2 of 6)
Methyl	27.2 % (273 of 1002)	27.5 % (138 of 501)	26.9 % (135 of 501)

1. ubiquitin receptor A

GPGSMTTSGA LFPSLVPGSR GASNKYLVEF RAGKMSLKGT TVTPDKRKGL VYIQQTDDSL IHFCWKDRTS GNVEDDLIIF PDDCEFKRVP QCPSGRVYVL KFKAGSKRLF FWMQEPKTDQ DEEHCRKVNE YLNNPP

2. ubiquitin receptor B

MPGALGASGS SGHELSALGP GSQEPEPPEP FEYIDD

3. ubiquitin receptor C

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGD

4. ubiquitin receptor D

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGRQL EDGRTLSDYN IQKESTLHLV LRLRGG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Rpn13	[U-13C]	0.6 mM
2	Rpn2	natural abundance	0.6 mM
3	proximal ubiquitin of Diubiquitin	[U-13C]	0.72 mM
4	proximal ubiquitin of Diubiquitin	[U-13C]	0.72 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	Rpn13	[U-13C]	0.6 mM
6	Rpn2	natural abundance	0.6 mM
7	distal ubiquitin of Diubiquitin	[U-13C]	0.72 mM
8	distal ubiquitin of Diubiquitin	[U-13C]	0.72 mM

Chem. Shift Complete4

Sequence coverage: 33.2 %, Completeness: 28.9 %, Completeness (bb): 29.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	28.9 % (4389 of 15212)	29.4 % (2347 of 7996)	28.5 % (1676 of 5888)	27.6 % (366 of 1328)
Backbone	29.0 % (2214 of 7624)	29.6 % (777 of 2628)	29.1 % (1102 of 3784)	27.6 % (335 of 1212)
Sidechain	29.1 % (2550 of 8772)	29.3 % (1573 of 5368)	28.7 % (945 of 3288)	27.6 % (32 of 116)
Aromatic	23.7 % (218 of 920)	27.6 % (127 of 460)	19.7 % (89 of 452)	25.0 % (2 of 8)
Methyl	29.8 % (398 of 1336)	30.4 % (203 of 668)	29.2 % (195 of 668)

1. ubiquitin receptor A

GPGSMTTSGA LFPSLVPGSR GASNKYLVEF RAGKMSLKGT TVTPDKRKGL VYIQQTDDSL IHFCWKDRTS GNVEDDLIIF PDDCEFKRVP QCPSGRVYVL KFKAGSKRLF FWMQEPKTDQ DEEHCRKVNE YLNNPP

2. ubiquitin receptor B

MPGALGASGS SGHELSALGP GSQEPEPPEP FEYIDD

3. ubiquitin receptor C

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGD

4. ubiquitin receptor D

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGRQL EDGRTLSDYN IQKESTLHLV LRLRGG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Rpn13	[U-13C]	0.6 mM
2	Rpn2	natural abundance	0.6 mM
3	proximal ubiquitin of Diubiquitin	[U-13C]	0.72 mM
4	proximal ubiquitin of Diubiquitin	[U-13C]	0.72 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	Rpn13	[U-13C]	0.6 mM
6	Rpn2	natural abundance	0.6 mM
7	distal ubiquitin of Diubiquitin	[U-13C]	0.72 mM
8	distal ubiquitin of Diubiquitin	[U-13C]	0.72 mM

Release date

2019-11-12

Citation

An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure
Lu, X., Ebelle, D.L., Matsuo, H., Walters, K.J.
Structure (2020), 28, 495-506, PubMed 32160516 , DOI 10.1016/j.str.2020.02.007 , Abstract

Related entities 1. ubiquitin receptor A, : 1 : 20 entities Detail

Related entities 2. ubiquitin receptor B, : 1 entities Detail

Related entities 3. ubiquitin receptor C, : 134 : 193 entities Detail

Related entities 4. ubiquitin receptor D, : 98 : 1 : 228 entities Detail

Experiments performed 4 experiments Detail

Chemical shift validation 9 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr28042_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: bmr28042_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1353	82.4 (chain: 1, length: 136)
2	Assigned chemical shifts	assigned_chem_shift_list_2	Warning	167	38.9 (chain: 2, length: 36)
3	Assigned chemical shifts	assigned_chem_shift_list_3	Warning	895	97.4 (chain: 3, length: 77)
4	Assigned chemical shifts	assigned_chem_shift_list_4	Warning	887	97.4 (chain: 4, length: 76)
1	Chemical shift references	chemical_shift_reference_1	OK	3	No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 136, Sequence coverage: 82.4%
- Total number of assignments
  - ¹H chemical shifts: 770
  - ¹³C chemical shifts: 483
  - ¹⁵N chemical shifts: 100
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1
Saveframe: assigned_chem_shift_list_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 36, Sequence coverage: 38.9%
- Total number of assignments
  - ¹H chemical shifts: 95
  - ¹³C chemical shifts: 61
  - ¹⁵N chemical shifts: 11
- Completeness of assignments
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 2
Saveframe: assigned_chem_shift_list_3
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 3, Chain length: 77, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 535
  - ¹³C chemical shifts: 312
  - ¹⁵N chemical shifts: 48
- Completeness of assignments
  - Entity_assemble_ID: 3
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 3
Saveframe: assigned_chem_shift_list_4
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 4, Chain length: 76, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 530
  - ¹³C chemical shifts: 309
  - ¹⁵N chemical shifts: 48
- Completeness of assignments
  - Entity_assemble_ID: 4
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	847	670	79.1
¹³C chemical shifts	625	483	77.3
¹⁵N chemical shifts	146	100	68.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	273	201	73.6
¹³C chemical shifts	272	217	79.8
¹⁵N chemical shifts	126	86	68.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	574	469	81.7
¹³C chemical shifts	353	266	75.4
¹⁵N chemical shifts	20	14	70.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	482	435	90.2
¹³C chemical shifts	353	312	88.4
¹⁵N chemical shifts	86	48	55.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	157	122	77.7
¹³C chemical shifts	154	120	77.9
¹⁵N chemical shifts	74	41	55.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	66	91.7
¹³C chemical shifts	70	41	58.6
¹⁵N chemical shifts	2	2	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	325	313	96.3
¹³C chemical shifts	199	192	96.5
¹⁵N chemical shifts	12	7	58.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	477	430	90.1
¹³C chemical shifts	349	309	88.5
¹⁵N chemical shifts	86	48	55.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	155	121	78.1
¹³C chemical shifts	152	119	78.3
¹⁵N chemical shifts	73	41	56.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	322	309	96.0
¹³C chemical shifts	197	190	96.4
¹⁵N chemical shifts	13	7	53.8

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Found 1 Document (0.801 seconds)

BMRB: 28042

Sample #1

Sample #2

Sample #1

Sample #2

Sample #1

Sample #2

Sample #1

Sample #2

Related entities 1. ubiquitin receptor A, : 1 : 20 entities Detail

Related entities 2. ubiquitin receptor B, : 1 entities Detail

Related entities 3. ubiquitin receptor C, : 134 : 193 entities Detail

Related entities 4. ubiquitin receptor D, : 98 : 1 : 228 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 9 contents Detail