- PDB-6u3s: Solution NMR structure of the DNAJB6b deltaST variant (Aligned on... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6u3s
Title
Solution NMR structure of the DNAJB6b deltaST variant (Aligned on the CTD domain)
Components
DnaJ homolog subfamily B member 6
Keywords
CHAPERONE / Hsp40 / Antiaggregation / amyloid
Function / homology
Function and homology information
chorion development / chorio-allantoic fusion / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / negative regulation of inclusion body assembly / intermediate filament organization / ATPase activator activity / protein localization to nucleus / Regulation of HSF1-mediated heat shock response / chaperone-mediated protein folding / regulation of cellular response to heat ...chorion development / chorio-allantoic fusion / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / negative regulation of inclusion body assembly / intermediate filament organization / ATPase activator activity / protein localization to nucleus / Regulation of HSF1-mediated heat shock response / chaperone-mediated protein folding / regulation of cellular response to heat / protein folding chaperone / Hsp70 protein binding / heat shock protein binding / extracellular matrix organization / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Z disc / regulation of protein localization / unfolded protein binding / protein folding / protein-folding chaperone binding / actin cytoskeleton organization / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / DNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function
Mass: 21831.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJB6, HSJ2, MRJ, MSJ1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75190
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
1
isotropic
2
2D 1H-15N TROSY
1
2
1
isotropic
2
3D HN(CA)CB
1
3
1
isotropic
2
3D HNCA
1
4
1
isotropic
1
3D HNCO
1
16
4
isotropic
2
3D HNCO
1
5
3
isotropic
2
2D 1H-13C HMQC
1
6
2
isotropic
2
2D 1H-13C HMQC constant time
1
7
2
isotropic
2
3DHMCMCBCA
1
8
2
isotropic
2
3DHMCM(CBCA)CO
1
9
5
isotropic
3
3D HHN NOESY-TROSY
1
10
3
isotropic
4
3D HHC NOESY-HMQC
1
11
3
isotropic
2
3D HHC HMQC-NOESY
1
12
3
isotropic
4
3D HCC HMQC-NOESY-HMQC
1
13
5
isotropic
1
2DHNPRE
2
14
6
anisotropic
3
2DHNARTSYPF1
1
17
7
anisotropic
3
2DHNARTSYPegHex
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Sample preparation
Details
Type
Solution-ID
Contents
Label
Solvent system
Details
solution
1
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, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2O
DCN_sample
90% H2O/10% D2O
solution
2
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
ILV_U13C_sample
100% D2O
Specifically protonated at CH3-ILV positions, uniformly 13C, 15N, 2H
solution
3
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
ILV_sample
100% D2O
Specifically protonated at CH3-ILV positions, uniformly 15N, 2H
solution
4
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
CN_sample
90% H2O/10% D2O
solution
5
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
DN_sample
90% H2O/10% D2O
filamentousvirus
6
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
PF1_sample
90% H2O/10% D2O
gelsolution
7
0.0002 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
Peg/Hex_sample
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.0002M
DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b
[U-13C; U-15N; U-2H]
1
0.05M
sodiumchloride
naturalabundance
1
0.02 % w/v
sodiumazide
naturalabundance
1
0.02M
sodiumphosphate
naturalabundance
1
0.0002M
DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b
[ILV-CH3; U-13C; U-15N; U-2H]
2
0.05M
sodiumchloride
naturalabundance
2
0.02 % w/v
sodiumazide
naturalabundance
2
0.02M
sodiumphosphate
naturalabundance
2
0.0002M
DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b
[ILV-CH3; U-15N; U-2H]
3
0.05M
sodiumchloride
naturalabundance
3
0.02 % w/v
sodiumazide
naturalabundance
3
0.02M
sodiumphosphate
naturalabundance
3
0.0002M
DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b