BMRBj - BMREntryMaster

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BMRB: 30655

6U3S

Solution NMR structure of the DNAJB6b deltaST variant (Aligned on the J domain)

Authors

Karamanos, T.K., Clore, G.M.

Assembly

DnaJ homolog subfamily B member 6

Entity

1. DnaJ homolog subfamily B member 6 (polymer, Thiol state: not present), 190 monomers, 21794.99 Da Detail

GMVDYYEVLG VQRHASPEDI KKAYRKLALK WHPDKNPENK EEAERKFKQV AEAYEVLSDA KKRDIYDKYG KEGLNGGGGG GSHFDSPFEF GFTFRNPDDV FREFFGGRDP FSFDFFEDPF EDFFGNRRGP RGGMGNFKSI STSTKMVNGR KITTKRIVEN GQERVEVEED GQLKSLTING KEQLLRLDNK

Formula weight

21794.99 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.2 %, Completeness: 43.8 %, Completeness (bb): 74.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	43.8 % (997 of 2276)	23.1 % (278 of 1205)	63.6 % (555 of 873)	82.8 % (164 of 198)
Backbone	74.6 % (838 of 1124)	46.4 % (183 of 394)	89.8 % (492 of 548)	89.6 % (163 of 182)
Sidechain	24.1 % (318 of 1320)	11.7 % (95 of 811)	45.0 % (222 of 493)	6.3 % (1 of 16)
Aromatic	2.5 % (6 of 242)	4.1 % (5 of 121)	0.0 % (0 of 120)	100.0 % (1 of 1)
Methyl	68.5 % (89 of 130)	63.1 % (41 of 65)	73.8 % (48 of 65)

1. entity 1

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [U-13C; U-15N; U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 5e-05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DNAJB6b deltaST variant	[U-13C; U-15N; U-2H]	2e-04 M
2	sodium chloride	natural abundance	5e-05 M
3	sodium azide	natural abundance	0.02 % w/v
4	sodium phosphate	natural abundance	0.02 M

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [ILV-CH3; U-13C; U-15N; U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 100% D2O

#	Name	Isotope labeling	Concentration
5	DNAJB6b deltaST variant	[ILV-CH3; U-13C; U-15N; U-2H]	2e-04 M
6	sodium chloride	natural abundance	0.05 M
7	sodium azide	natural abundance	0.02 % w/v
8	sodium phosphate	natural abundance	0.02 M

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [ILV-CH3; U-15N; U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 100% D2O

#	Name	Isotope labeling	Concentration
9	DNAJB6b deltaST variant	[ILV-CH3; U-15N; U-2H]	2e-04 M
10	sodium chloride	natural abundance	0.05 M
11	sodium azide	natural abundance	0.02 % w/v
12	sodium phosphate	natural abundance	0.02 M

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [U-13C; U-15N] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DNAJB6b deltaST variant	[U-13C; U-15N]	2e-04 M
14	sodium chloride	natural abundance	0.05 M
15	sodium azide	natural abundance	0.02 % w/v
16	sodium phosphate	natural abundance	0.02 M

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [U-15N;U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
17	DNAJB6b deltaST variant	[U-15N;U-2H]	2e-04 M
18	sodium chloride	natural abundance	0.05 M
19	sodium azide	natural abundance	0.02 % w/v
20	sodium phosphate	natural abundance	0.02 M

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [U-15N;U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.1 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
21	DNAJB6b deltaST variant	[U-15N;U-2H]	2e-04 M
22	sodium chloride	natural abundance	0.1 M
23	sodium azide	natural abundance	0.02 % w/v
24	sodium phosphate	natural abundance	0.02 M

Sample #7

#	Name	Isotope labeling	Concentration
25	DNAJB6b deltaST variant	[U-15N;U-2H]	2e-04 M
26	sodium chloride	natural abundance	0.05 M
27	sodium azide	natural abundance	0.02 % w/v
28	sodium phosphate	natural abundance	2e-05 M

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹⁵C	water	protons	4.78 ppm	internal	indirect	0.101
¹H	water	protons	4.78 ppm	internal	direct	1.0
¹³N	water	protons	4.78 ppm	internal	indirect	0.251

Referencing offset: -0.2 ppm, Outliers: 5 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹⁵C	water	protons	4.78 ppm	internal	indirect	0.101
¹H	water	protons	4.78 ppm	internal	direct	1.0
¹³N	water	protons	4.78 ppm	internal	indirect	0.251

Referencing offset: -0.2 ppm, Outliers: 5 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹⁵C	water	protons	4.78 ppm	internal	indirect	0.101
¹H	water	protons	4.78 ppm	internal	direct	1.0
¹³N	water	protons	4.78 ppm	internal	indirect	0.251

Referencing offset: 0.02 ppm, Outliers: 7 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 6U3R, Strand ID: A Detail

Release date

2019-09-17

Citation

Unraveling the structure and dynamics of the human DNAJB6b chaperone by NMR reveals insights into Hsp40-mediated proteostasis
Karamanos, T.K., Tugarinov, V.T., Clore, G.M.
Proc. Natl. Acad. Sci. U. S. A. (2019), 116, 21529-21538, PubMed 31591220 , DOI 10.1073/pnas.1914999116 , Abstract

Related entities 1. DnaJ homolog subfamily B member 6, : 1 : 1 : 39 entities Detail

Interaction partners 1. DnaJ homolog subfamily B member 6, : 8 interactors Detail

More details for 8 interactors identified by 5 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N TROSY

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [U-13C; U-15N; U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 5e-05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DNAJB6b deltaST variant	[U-13C; U-15N; U-2H]	2e-04 M
2	sodium chloride	natural abundance	5e-05 M
3	sodium azide	natural abundance	0.02 % w/v
4	sodium phosphate	natural abundance	0.02 M

2 3D HNCACB

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DNAJB6b deltaST variant	[U-13C; U-15N; U-2H]	2e-04 M
2	sodium chloride	natural abundance	5e-05 M
3	sodium azide	natural abundance	0.02 % w/v
4	sodium phosphate	natural abundance	0.02 M

3 3D HNCA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DNAJB6b deltaST variant	[U-13C; U-15N; U-2H]	2e-04 M
2	sodium chloride	natural abundance	5e-05 M
3	sodium azide	natural abundance	0.02 % w/v
4	sodium phosphate	natural abundance	0.02 M

4 3D HNCO

Instrument

Bruker AVANCE III - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DNAJB6b deltaST variant	[U-13C; U-15N; U-2H]	2e-04 M
2	sodium chloride	natural abundance	5e-05 M
3	sodium azide	natural abundance	0.02 % w/v
4	sodium phosphate	natural abundance	0.02 M

5 2D 1H-13C HMQC

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [ILV-CH3; U-15N; U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 100% D2O

#	Name	Isotope labeling	Concentration
9	DNAJB6b deltaST variant	[ILV-CH3; U-15N; U-2H]	2e-04 M
10	sodium chloride	natural abundance	0.05 M
11	sodium azide	natural abundance	0.02 % w/v
12	sodium phosphate	natural abundance	0.02 M

6 3D HMCM(CBCA)CO

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [ILV-CH3; U-13C; U-15N; U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 100% D2O

#	Name	Isotope labeling	Concentration
5	DNAJB6b deltaST variant	[ILV-CH3; U-13C; U-15N; U-2H]	2e-04 M
6	sodium chloride	natural abundance	0.05 M
7	sodium azide	natural abundance	0.02 % w/v
8	sodium phosphate	natural abundance	0.02 M

7 3D HHN NOESY-TROSY

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [U-15N;U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
17	DNAJB6b deltaST variant	[U-15N;U-2H]	2e-04 M
18	sodium chloride	natural abundance	0.05 M
19	sodium azide	natural abundance	0.02 % w/v
20	sodium phosphate	natural abundance	0.02 M

8 3D HHC NOESY-HMQC

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
9	DNAJB6b deltaST variant	[ILV-CH3; U-15N; U-2H]	2e-04 M
10	sodium chloride	natural abundance	0.05 M
11	sodium azide	natural abundance	0.02 % w/v
12	sodium phosphate	natural abundance	0.02 M

9 3D HHC HMQC-NOESY

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
9	DNAJB6b deltaST variant	[ILV-CH3; U-15N; U-2H]	2e-04 M
10	sodium chloride	natural abundance	0.05 M
11	sodium azide	natural abundance	0.02 % w/v
12	sodium phosphate	natural abundance	0.02 M

10 3D HMCMCBCA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	DNAJB6b deltaST variant	[ILV-CH3; U-13C; U-15N; U-2H]	2e-04 M
6	sodium chloride	natural abundance	0.05 M
7	sodium azide	natural abundance	0.02 % w/v
8	sodium phosphate	natural abundance	0.02 M

11 3D HCC HMQC-NOESY-HMQC

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
9	DNAJB6b deltaST variant	[ILV-CH3; U-15N; U-2H]	2e-04 M
10	sodium chloride	natural abundance	0.05 M
11	sodium azide	natural abundance	0.02 % w/v
12	sodium phosphate	natural abundance	0.02 M

12 2D HN PRE

Instrument

Bruker AVANCE III - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DNAJB6b deltaST variant	[U-15N;U-2H]	2e-04 M
18	sodium chloride	natural abundance	0.05 M
19	sodium azide	natural abundance	0.02 % w/v
20	sodium phosphate	natural abundance	0.02 M

13 3D HNCO

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [U-13C; U-15N] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DNAJB6b deltaST variant	[U-13C; U-15N]	2e-04 M
14	sodium chloride	natural abundance	0.05 M
15	sodium azide	natural abundance	0.02 % w/v
16	sodium phosphate	natural abundance	0.02 M

14 2D 1H-13C HMQC constant time

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	DNAJB6b deltaST variant	[ILV-CH3; U-13C; U-15N; U-2H]	2e-04 M
6	sodium chloride	natural abundance	0.05 M
7	sodium azide	natural abundance	0.02 % w/v
8	sodium phosphate	natural abundance	0.02 M

15 2D HN ARTSY PF1

Instrument

Bruker AVANCE III - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7 (±0.1), Details 2e-04 M [U-15N;U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.1 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
21	DNAJB6b deltaST variant	[U-15N;U-2H]	2e-04 M
22	sodium chloride	natural abundance	0.1 M
23	sodium azide	natural abundance	0.02 % w/v
24	sodium phosphate	natural abundance	0.02 M

16 2D HN ARTSY PegHex

Instrument

Bruker AVANCE III - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 2e-04 M [U-15N;U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 2e-05 M sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
25	DNAJB6b deltaST variant	[U-15N;U-2H]	2e-04 M
26	sodium chloride	natural abundance	0.05 M
27	sodium azide	natural abundance	0.02 % w/v
28	sodium phosphate	natural abundance	2e-05 M

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30655_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: bmr30655_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	977		92.6 (chain: 1, length: 190)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 190, Sequence coverage: 92.6%
- Total number of assignments
  - ¹³C chemical shifts: 535
  - ¹H chemical shifts: 283
  - ¹⁵N chemical shifts: 159
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	873	535	61.3
¹H chemical shifts	1205	201	16.7
¹⁵N chemical shifts	212	159	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	380	326	85.8
¹H chemical shifts	394	159	40.4
¹⁵N chemical shifts	182	158	86.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	493	209	42.4
¹H chemical shifts	811	42	5.2
¹⁵N chemical shifts	30	1	3.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	68	48	70.6
¹H chemical shifts	68	41	60.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	120	0	0.0
¹H chemical shifts	121	1	0.8
¹⁵N chemical shifts	1	1	100.0

Keywords Anti-aggregation, CHAPERONE, Hsp40, amyloid

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Found 1 Document (2.083 seconds)

BMRB: 30655

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Sample #7

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DnaJ homolog subfamily B member 6, : 1 : 1 : 39 entities Detail

Interaction partners 1. DnaJ homolog subfamily B member 6, : 8 interactors Detail

Experiments performed 16 experiments Detail

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Chemical shift validation 3 contents Detail