BMRB Entry 30656

Name: Solution NMR structure of the DNAJB6b deltaST variant (Aligned on the CTD domain)
Published: 2019-10-04

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PDB ID: 6u3s
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30656
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2019-08-22

Original release date:

2019-10-04

Authors:

Karamanos, T.; Clore, G.

Citation:

Citation: Karamanos, T.; Tugarinov, V.; Clore, G.. "Unraveling the structure and dynamics of the human DNAJB6b chaperone by NMR reveals insights into Hsp40-mediated proteostasis" Proc. Natl. Acad. Sci. U. S. A. 116, 21529-21538 (2019).
PubMed: 31591220

Assembly members:

Assembly members:
entity_1, polymer, 190 residues, 21831.303 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GMVDYYEVLGVQRHASPEDI KKAYRKLALKWHPDKNPENK EEAERKFKQVAEAYEVLSDA KKRDIYDKYGKEGLNGGGGG GSHFDSPFEFGFTFRNPDDV FREFFGGRDPFSFDFFEDPF EDFFGNRRGPRGGMGNFKSI STSTKMVNGRKITTKRIVEN GQERVEVEEDGQLKSLTING KEQLLRLDNK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	535
15N chemical shifts	159
1H chemical shifts	283

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 190 residues - 21831.303 Da.

1	GLY	MET	VAL	ASP	TYR	TYR	GLU	VAL	LEU	GLY
2	VAL	GLN	ARG	HIS	ALA	SER	PRO	GLU	ASP	ILE
3	LYS	LYS	ALA	TYR	ARG	LYS	LEU	ALA	LEU	LYS
4	TRP	HIS	PRO	ASP	LYS	ASN	PRO	GLU	ASN	LYS
5	GLU	GLU	ALA	GLU	ARG	LYS	PHE	LYS	GLN	VAL
6	ALA	GLU	ALA	TYR	GLU	VAL	LEU	SER	ASP	ALA
7	LYS	LYS	ARG	ASP	ILE	TYR	ASP	LYS	TYR	GLY
8	LYS	GLU	GLY	LEU	ASN	GLY	GLY	GLY	GLY	GLY
9	GLY	SER	HIS	PHE	ASP	SER	PRO	PHE	GLU	PHE
10	GLY	PHE	THR	PHE	ARG	ASN	PRO	ASP	ASP	VAL
11	PHE	ARG	GLU	PHE	PHE	GLY	GLY	ARG	ASP	PRO
12	PHE	SER	PHE	ASP	PHE	PHE	GLU	ASP	PRO	PHE
13	GLU	ASP	PHE	PHE	GLY	ASN	ARG	ARG	GLY	PRO
14	ARG	GLY	GLY	MET	GLY	ASN	PHE	LYS	SER	ILE
15	SER	THR	SER	THR	LYS	MET	VAL	ASN	GLY	ARG
16	LYS	ILE	THR	THR	LYS	ARG	ILE	VAL	GLU	ASN
17	GLY	GLN	GLU	ARG	VAL	GLU	VAL	GLU	GLU	ASP
18	GLY	GLN	LEU	LYS	SER	LEU	THR	ILE	ASN	GLY
19	LYS	GLU	GLN	LEU	LEU	ARG	LEU	ASP	ASN	LYS

Samples:

sample_1: DNAJB6b deltaST variant, [U-13C; U-15N; U-2H], 2e-04 M; sodium chloride 0.05 M; sodium azide 0.02 % w/v; sodium phosphate 0.02 M

sample_2: DNAJB6b deltaST variant, [ILV-CH3; U-13C; U-15N; U-2H], 2e-04 M; sodium chloride 0.05 M; sodium azide 0.02 % w/v; sodium phosphate 0.02 M

sample_3: DNAJB6b deltaST variant, [ILV-CH3; U-15N; U-2H], 2e-04 M; sodium chloride 0.05 M; sodium azide 0.02 % w/v; sodium phosphate 0.02 M

sample_4: DNAJB6b deltaST variant, [U-13C; U-15N], 2e-04 M; sodium chloride 0.05 M; sodium azide 0.02 % w/v; sodium phosphate 0.02 M

sample_5: DNAJB6b deltaST variant, [U-15N;U-2H], 2e-04 M; sodium chloride 0.05 M; sodium azide 0.02 % w/v; sodium phosphate 0.02 M

sample_6: DNAJB6b deltaST variant, [U-15N;U-2H], 2e-04 M; sodium chloride 0.1 M; sodium azide 0.02 % w/v; sodium phosphate 0.02 M

sample_7: DNAJB6b deltaST variant, [U-15N;U-2H], 0.0002 M; sodium chloride 0.05 M; sodium azide 0.02 % w/v; sodium phosphate 0.02 M

sample_conditions_1: ionic strength: 87 mM; pH: 6.7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 145 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HMQC constant time	sample_2	isotropic	sample_conditions_1
3D HMCMCBCA	sample_2	isotropic	sample_conditions_1
3D HMCM(CBCA)CO	sample_2	isotropic	sample_conditions_1
3D HHN NOESY-TROSY	sample_5	isotropic	sample_conditions_1
3D HHC NOESY-HMQC	sample_3	isotropic	sample_conditions_1
3D HHC HMQC-NOESY	sample_3	isotropic	sample_conditions_1
3D HCC HMQC-NOESY-HMQC	sample_3	isotropic	sample_conditions_1
2D HN PRE	sample_5	isotropic	sample_conditions_1
2D HN ARTSY PF1	sample_6	anisotropic	sample_conditions_2
3D HNCO	sample_4	isotropic	sample_conditions_1
2D HN ARTSY PegHex	sample_7	anisotropic	sample_conditions_1

Software:

CS-ROSETTA, Shen, Vernon, Baker and Bax - refinement, structure calculation

CcpNmr Analysis, CCPN - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

Bruker AVANCE III 500 MHz
Bruker AVANCE III 600 MHz
Bruker AVANCE III 800 MHz
Bruker AVANCE III 900 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

1	GLY	MET	VAL	ASP	TYR	TYR	GLU	VAL	LEU	GLY
2	VAL	GLN	ARG	HIS	ALA	SER	PRO	GLU	ASP	ILE
3	LYS	LYS	ALA	TYR	ARG	LYS	LEU	ALA	LEU	LYS
4	TRP	HIS	PRO	ASP	LYS	ASN	PRO	GLU	ASN	LYS
5	GLU	GLU	ALA	GLU	ARG	LYS	PHE	LYS	GLN	VAL
6	ALA	GLU	ALA	TYR	GLU	VAL	LEU	SER	ASP	ALA
7	LYS	LYS	ARG	ASP	ILE	TYR	ASP	LYS	TYR	GLY
8	LYS	GLU	GLY	LEU	ASN	GLY	GLY	GLY	GLY	GLY
9	GLY	SER	HIS	PHE	ASP	SER	PRO	PHE	GLU	PHE
10	GLY	PHE	THR	PHE	ARG	ASN	PRO	ASP	ASP	VAL
11	PHE	ARG	GLU	PHE	PHE	GLY	GLY	ARG	ASP	PRO
12	PHE	SER	PHE	ASP	PHE	PHE	GLU	ASP	PRO	PHE
13	GLU	ASP	PHE	PHE	GLY	ASN	ARG	ARG	GLY	PRO
14	ARG	GLY	GLY	MET	GLY	ASN	PHE	LYS	SER	ILE
15	SER	THR	SER	THR	LYS	MET	VAL	ASN	GLY	ARG
16	LYS	ILE	THR	THR	LYS	ARG	ILE	VAL	GLU	ASN
17	GLY	GLN	GLU	ARG	VAL	GLU	VAL	GLU	GLU	ASP
18	GLY	GLN	LEU	LYS	SER	LEU	THR	ILE	ASN	GLY
19	LYS	GLU	GLN	LEU	LEU	ARG	LEU	ASP	ASN	LYS

1	GLY	MET	VAL	ASP	TYR	TYR	GLU	VAL	LEU	GLY
2	VAL	GLN	ARG	HIS	ALA	SER	PRO	GLU	ASP	ILE
3	LYS	LYS	ALA	TYR	ARG	LYS	LEU	ALA	LEU	LYS
4	TRP	HIS	PRO	ASP	LYS	ASN	PRO	GLU	ASN	LYS
5	GLU	GLU	ALA	GLU	ARG	LYS	PHE	LYS	GLN	VAL
6	ALA	GLU	ALA	TYR	GLU	VAL	LEU	SER	ASP	ALA
7	LYS	LYS	ARG	ASP	ILE	TYR	ASP	LYS	TYR	GLY
8	LYS	GLU	GLY	LEU	ASN	GLY	GLY	GLY	GLY	GLY
9	GLY	SER	HIS	PHE	ASP	SER	PRO	PHE	GLU	PHE
10	GLY	PHE	THR	PHE	ARG	ASN	PRO	ASP	ASP	VAL
11	PHE	ARG	GLU	PHE	PHE	GLY	GLY	ARG	ASP	PRO
12	PHE	SER	PHE	ASP	PHE	PHE	GLU	ASP	PRO	PHE
13	GLU	ASP	PHE	PHE	GLY	ASN	ARG	ARG	GLY	PRO
14	ARG	GLY	GLY	MET	GLY	ASN	PHE	LYS	SER	ILE
15	SER	THR	SER	THR	LYS	MET	VAL	ASN	GLY	ARG
16	LYS	ILE	THR	THR	LYS	ARG	ILE	VAL	GLU	ASN
17	GLY	GLN	GLU	ARG	VAL	GLU	VAL	GLU	GLU	ASP
18	GLY	GLN	LEU	LYS	SER	LEU	THR	ILE	ASN	GLY
19	LYS	GLU	GLN	LEU	LEU	ARG	LEU	ASP	ASN	LYS

1	GLY	MET	VAL	ASP	TYR	TYR	GLU	VAL	LEU	GLY
2	VAL	GLN	ARG	HIS	ALA	SER	PRO	GLU	ASP	ILE
3	LYS	LYS	ALA	TYR	ARG	LYS	LEU	ALA	LEU	LYS
4	TRP	HIS	PRO	ASP	LYS	ASN	PRO	GLU	ASN	LYS
5	GLU	GLU	ALA	GLU	ARG	LYS	PHE	LYS	GLN	VAL
6	ALA	GLU	ALA	TYR	GLU	VAL	LEU	SER	ASP	ALA
7	LYS	LYS	ARG	ASP	ILE	TYR	ASP	LYS	TYR	GLY
8	LYS	GLU	GLY	LEU	ASN	GLY	GLY	GLY	GLY	GLY
9	GLY	SER	HIS	PHE	ASP	SER	PRO	PHE	GLU	PHE
10	GLY	PHE	THR	PHE	ARG	ASN	PRO	ASP	ASP	VAL
11	PHE	ARG	GLU	PHE	PHE	GLY	GLY	ARG	ASP	PRO
12	PHE	SER	PHE	ASP	PHE	PHE	GLU	ASP	PRO	PHE
13	GLU	ASP	PHE	PHE	GLY	ASN	ARG	ARG	GLY	PRO
14	ARG	GLY	GLY	MET	GLY	ASN	PHE	LYS	SER	ILE
15	SER	THR	SER	THR	LYS	MET	VAL	ASN	GLY	ARG
16	LYS	ILE	THR	THR	LYS	ARG	ILE	VAL	GLU	ASN
17	GLY	GLN	GLU	ARG	VAL	GLU	VAL	GLU	GLU	ASP
18	GLY	GLN	LEU	LYS	SER	LEU	THR	ILE	ASN	GLY
19	LYS	GLU	GLN	LEU	LEU	ARG	LEU	ASP	ASN	LYS