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BMRB: 25979

6CO4

protein complex

Authors

Lu, X., Walters, K.

Assembly

ADRM1-RPN2 complex

Entity

1. ADRM1-RPN2 complex, entity 1 (polymer, Thiol state: all free), 113 monomers, 13277.00 Da Detail

NKYLVEFRAG KMSLKGTTVT PDKRKGLVYI QQTDDSLIHF CWKDRTSGNV EDDLIIFPDD CEFKRVPQCP SGRVYVLKFK AGSKRLFFWM QEPKTDQDEE HCRKVNEYLN NPP

2. ADRM1-RPN2 complex, entity 2 (polymer, Thiol state: not present), 14 monomers, 1704.738 Da Detail

QEPEPPEPFE YIDD

Total weight

14981.738 Da

Max. entity weight

13277.0 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 88.2 %, Completeness: 80.3 %, Completeness (bb): 86.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.3 % (1251 of 1557)	78.3 % (646 of 825)	81.4 % (491 of 603)	88.4 % (114 of 129)
Backbone	86.9 % (643 of 740)	85.9 % (214 of 249)	86.9 % (326 of 375)	88.8 % (103 of 116)
Sidechain	76.0 % (713 of 938)	75.0 % (432 of 576)	77.4 % (270 of 349)	84.6 % (11 of 13)
Aromatic	55.3 % (84 of 152)	60.5 % (46 of 76)	48.6 % (36 of 74)	100.0 % (2 of 2)
Methyl	94.0 % (94 of 100)	94.0 % (47 of 50)	94.0 % (47 of 50)

1. entity 1

NKYLVEFRAG KMSLKGTTVT PDKRKGLVYI QQTDDSLIHF CWKDRTSGNV EDDLIIFPDD CEFKRVPQCP SGRVYVLKFK AGSKRLFFWM QEPKTDQDEE HCRKVNEYLN NPP

2. entity 2

QEPEPPEPFE YIDD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]	protein	0.7 mM
2	entity_2	[U-13C; U-15N]	protein	0.7 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	DTT	natural abundance		2 mM
6	sodium azide	natural abundance		0.1 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
9	entity_1	[U-13C; U-15N]	protein	0.7 mM
10	entity_2	[U-13C; U-15N]	protein	0.7 mM
11	potassium phosphate	natural abundance	buffer	20 mM
12	sodium chloride	natural abundance	salt	50 mM
13	DTT	natural abundance		2 mM
14	sodium azide	natural abundance		0.1 %
15	D2O	[U-2H]		100 %

Chem. Shift Complete2

Sequence coverage: 26.8 %, Completeness: 48.9 %, Completeness (bb): 54.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	48.9 % (1522 of 3114)	47.3 % (780 of 1650)	49.7 % (599 of 1206)	55.4 % (143 of 258)
Backbone	54.6 % (808 of 1480)	53.4 % (266 of 498)	54.8 % (411 of 750)	56.5 % (131 of 232)
Sidechain	45.1 % (847 of 1876)	44.6 % (514 of 1152)	46.0 % (321 of 698)	46.2 % (12 of 26)
Aromatic	31.6 % (96 of 304)	34.9 % (53 of 152)	27.7 % (41 of 148)	50.0 % (2 of 4)
Methyl	53.0 % (106 of 200)	55.0 % (55 of 100)	51.0 % (51 of 100)

1. entity 1

NKYLVEFRAG KMSLKGTTVT PDKRKGLVYI QQTDDSLIHF CWKDRTSGNV EDDLIIFPDD CEFKRVPQCP SGRVYVLKFK AGSKRLFFWM QEPKTDQDEE HCRKVNEYLN NPP

2. entity 2

QEPEPPEPFE YIDD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]	protein	0.7 mM
2	entity_2	[U-13C; U-15N]	protein	0.7 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	DTT	natural abundance		2 mM
6	sodium azide	natural abundance		0.1 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
9	entity_1	[U-13C; U-15N]	protein	0.7 mM
10	entity_2	[U-13C; U-15N]	protein	0.7 mM
11	potassium phosphate	natural abundance	buffer	20 mM
12	sodium chloride	natural abundance	salt	50 mM
13	DTT	natural abundance		2 mM
14	sodium azide	natural abundance		0.1 %
15	D2O	[U-2H]		100 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2NBK, Strand ID: A, B Detail

Release date

2016-03-09

Citation

Structure of the Rpn13-Rpn2 complex provides insights for Rpn13 and Uch37 as anticancer targets
Lu, X., Nowicka, U., Sridharan, V., Liu, F., Randles, L., Hymel, D., Dyba, M., Tarasov, S.G., Tarasova, N.I., Zhao, X.Z., Hamazaki, J., Murata, S., Burke, T.R., Walters, K.J.
Nat. Commun. (2017), 8, 15540-15540, PubMed 28598414 , DOI 10.1038/ncomms15540 , Abstract

Related entities 1. ADRM1-RPN2 complex, entity 1, : 1 : 3 : 23 entities Detail

Related entities 2. ADRM1-RPN2 complex, entity 2, : 16 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]	protein	0.7 mM
2	entity_2	[U-13C; U-15N]	protein	0.7 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	DTT	natural abundance		2 mM
6	sodium azide	natural abundance		0.1 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

2 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]	protein	0.7 mM
2	entity_2	[U-13C; U-15N]	protein	0.7 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	DTT	natural abundance		2 mM
6	sodium azide	natural abundance		0.1 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]	protein	0.7 mM
2	entity_2	[U-13C; U-15N]	protein	0.7 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	DTT	natural abundance		2 mM
6	sodium azide	natural abundance		0.1 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]	protein	0.7 mM
2	entity_2	[U-13C; U-15N]	protein	0.7 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	DTT	natural abundance		2 mM
6	sodium azide	natural abundance		0.1 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]	protein	0.7 mM
2	entity_2	[U-13C; U-15N]	protein	0.7 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	DTT	natural abundance		2 mM
6	sodium azide	natural abundance		0.1 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
9	entity_1	[U-13C; U-15N]	protein	0.7 mM
10	entity_2	[U-13C; U-15N]	protein	0.7 mM
11	potassium phosphate	natural abundance	buffer	20 mM
12	sodium chloride	natural abundance	salt	50 mM
13	DTT	natural abundance		2 mM
14	sodium azide	natural abundance		0.1 %
15	D2O	[U-2H]		100 %

7 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
9	entity_1	[U-13C; U-15N]	protein	0.7 mM
10	entity_2	[U-13C; U-15N]	protein	0.7 mM
11	potassium phosphate	natural abundance	buffer	20 mM
12	sodium chloride	natural abundance	salt	50 mM
13	DTT	natural abundance		2 mM
14	sodium azide	natural abundance		0.1 %
15	D2O	[U-2H]		100 %

8 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
9	entity_1	[U-13C; U-15N]	protein	0.7 mM
10	entity_2	[U-13C; U-15N]	protein	0.7 mM
11	potassium phosphate	natural abundance	buffer	20 mM
12	sodium chloride	natural abundance	salt	50 mM
13	DTT	natural abundance		2 mM
14	sodium azide	natural abundance		0.1 %
15	D2O	[U-2H]		100 %

9 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]	protein	0.7 mM
2	entity_2	[U-13C; U-15N]	protein	0.7 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	DTT	natural abundance		2 mM
6	sodium azide	natural abundance		0.1 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

10 3D half-filtered NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
9	entity_1	[U-13C; U-15N]	protein	0.7 mM
10	entity_2	[U-13C; U-15N]	protein	0.7 mM
11	potassium phosphate	natural abundance	buffer	20 mM
12	sodium chloride	natural abundance	salt	50 mM
13	DTT	natural abundance		2 mM
14	sodium azide	natural abundance		0.1 %
15	D2O	[U-2H]		100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25979_6co4.nef
Input source #2: Coordindates	6co4.cif
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

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

------------10--------20--------30--------40--------50--------60--------70--------80--------90------
GPGSMTTSGALFPSLVPGSRGASNKYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGNVEDDLIIFPDDCEFKRVPQCPSGRVYVL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPGSMTTSGALFPSLVPGSRGASNKYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGNVEDDLIIFPDDCEFKRVPQCPSGRVYVL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-100-------110-------120-------130-------140-------150
KFKAGSKRLFFWMQEPKTDQDEEHCRKVNEYLNNPPMPGALGASGSSGHELSAL
||||||||||||||||||||||||||||||||||||||||||||||||||||||
KFKAGSKRLFFWMQEPKTDQDEEHCRKVNEYLNNPPMPGALGASGSSGHELSAL
-------110-------120-------130-------140-------150----

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--940-------950---
GPGSQEPEPPEPFEYIDD
||||||||||||||||||
GPGSQEPEPPEPFEYIDD
--------10--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	154	0	0	100.0
B	B	18	0	0	100.0

Content subtype: combined_25979_6co4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1253		72.7 (chain: A, length: 154)
2	Assigned chemical shifts	assigned_chem_shift_list_2	Warning	154		77.8 (chain: B, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	5648 (1)	noe	73.4 (chain: A, length: 154), 77.8 (chain: B, length: 18)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	86 (1)	hbond	29.9 (chain: A, length: 154), 5.6 (chain: B, length: 18)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	200 (200)	.	70.8 (chain: A, length: 154), 72.2 (chain: B, length: 18)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 154, Sequence coverage: 72.7%
- Total number of assignments
  - ¹H chemical shifts: 649
  - ¹³C chemical shifts: 487
  - ¹⁵N chemical shifts: 117
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A
Saveframe: assigned_chem_shift_list_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 77.8%
- Total number of assignments
  - ¹H chemical shifts: 85
  - ¹³C chemical shifts: 58
  - ¹⁵N chemical shifts: 11
- Completeness of assignments
  - Entity_assemble_ID: B
- 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: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	931	649	69.7
¹³C chemical shifts	691	487	70.5
¹⁵N chemical shifts	163	117	71.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	312	218	69.9
¹³C chemical shifts	308	221	71.8
¹⁵N chemical shifts	143	103	72.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	619	431	69.6
¹³C chemical shifts	383	266	69.5
¹⁵N chemical shifts	20	14	70.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	49	69.0
¹³C chemical shifts	71	49	69.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	45	60.8
¹³C chemical shifts	72	33	45.8
¹⁵N chemical shifts	2	2	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
950	TYR	HH	7.05

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	109	84	77.1
¹³C chemical shifts	79	58	73.4
¹⁵N chemical shifts	14	11	78.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	33	23	69.7
¹³C chemical shifts	36	25	69.4
¹⁵N chemical shifts	13	10	76.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	61	80.3
¹³C chemical shifts	43	33	76.7
¹⁵N chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	2	100.0
¹³C chemical shifts	2	2	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	5	55.6
¹³C chemical shifts	9	3	33.3

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 154, Sequence coverage: 73.4%
  - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 77.8%
- Total number of restraints: 5645
- Weight of restraints: 1.0 (5645)
- Potential type of restraints: square-well-parabolic (5645)
- Range of distance target values: 2.4, 4.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 154, Sequence coverage: 29.9%
    - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 5.6%
  - Total number of restraints: 86
  - Weight of restraints: 1.0 (86)
  - Potential type of restraints: square-well-parabolic (86)
  - Range of distance target values: 2.15, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 154, Sequence coverage: 70.8%
  - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 72.2%
- Total number of restraints: 200
- Total number of restraints per polymer type: 200
- Weight of restraints: 1.0 (200)
- Potential type of restraints: square-well-parabolic (200)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords protein binding

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Found 1 Document (0.802 seconds)

BMRB: 25979

Sample #1

Sample #2

Sample #1

Sample #2

Related entities 1. ADRM1-RPN2 complex, entity 1, : 1 : 3 : 23 entities Detail

Related entities 2. ADRM1-RPN2 complex, entity 2, : 16 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 6 contents Detail