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6z5n

DnaJB1 JD-GF

Method: SOLUTION NMR Dmax: 49.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DnaJ homolog subfamily B member 1

Homo sapiens

UniProt P25685

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–110 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1 NMR sample composition：4.0 mM [U-13C; U-15N] DnaJB1 JD-GF, 2.0 mM [U-15N] DnaJB1 JD-GF, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.4 mM [U-15N] DnaJB1 JD-GF, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：2.5 mM [U-13C; U-15N] DnaJB1 JD-GF, 100% D2O | 100% D2O NMR sample composition：4.0 mM [U-13C; U-15N] DnaJB1 JD-GF, 2.0 mM [U-15N] DnaJB1 JD-GF, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6Z5N Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1HDJ HUMAN HSP40 (HDJ-1), NMR Deposited 1996-05-09 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：J-DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；303 K
Resolution not provided
2QLD human Hsp40 Hdj1 Deposited 2007-07-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 158–340（183 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；100mM Citric buffer, PEG400 25%, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.70 Å R-free 0.336
3AGX Crystal structure of human Hsp40 Hdj1 peptide-binding domain Deposited 2010-04-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 161–340（180 aa） Fragment：UNP residues 161-340
Chain B 161–340（180 aa） Fragment：UNP residues 161-340
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；13% PEG 3350, 0.1M Na citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.85 Å R-free 0.247
3AGY Crystal structure of human Hsp40 Hdj1 peptide-binding domain complexed with a C-terminal peptide of Hsp70 Deposited 2010-04-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 161–340（180 aa） Fragment：UNP residues 161-340
Chain B 161–340（180 aa） Fragment：UNP residues 161-340
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；18% PEG 3350, 0.1M Na citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.85 Å R-free 0.247
3AGZ Crystal structure of human Hsp40 Hdj1 peptide-binding domain complexed with a C-terminal peptide of Hsp70 Deposited 2010-04-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 151–340（190 aa） Fragment：UNP residues 151-340
Chain B 151–340（190 aa） Fragment：UNP residues 151-340
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；277 K；18% PEG 3350, 0.1M CHES, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.51 Å R-free 0.269
4WB7 Crystal structure of a chimeric fusion of human DnaJ (Hsp40) and cAMP-dependent protein kinase A (catalytic alpha subunit) Deposited 2014-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–70（69 aa） Fragment：UNP P25685 residues 2-70,UNP P17612 residues 16-351
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；70mM sodium cacodylate pH 6.5, 150mM magnesium acetate, 20mM zinc chloride, 5% glycerol, 11.5% PEG 8000
Resolution 1.90 Å R-free 0.188
4WB7 Crystal structure of a chimeric fusion of human DnaJ (Hsp40) and cAMP-dependent protein kinase A (catalytic alpha subunit) Deposited 2014-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–70（69 aa） Fragment：UNP P25685 residues 2-70,UNP P17612 residues 16-351
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；70mM sodium cacodylate pH 6.5, 150mM magnesium acetate, 20mM zinc chloride, 5% glycerol, 11.5% PEG 8000
Resolution 1.90 Å R-free 0.188
6BYR Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PKAc alpha Deposited 2017-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–70（69 aa）
Chain C 2–70（69 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM NaCl, 16-18% pentaerythritol propoxylate and 10% dimethyl sulfoxide
Resolution 3.66 Å R-free 0.249
6BYR Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PKAc alpha Deposited 2017-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–70（69 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM NaCl, 16-18% pentaerythritol propoxylate and 10% dimethyl sulfoxide
Resolution 3.66 Å R-free 0.249
6BYR Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PKAc alpha Deposited 2017-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–70（69 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM NaCl, 16-18% pentaerythritol propoxylate and 10% dimethyl sulfoxide
Resolution 3.66 Å R-free 0.249
6WJF PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar hepatoceullar carcinoma Deposited 2020-04-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–70（69 aa）
Chain B 2–70（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.50 Å
6WJG PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar hepatoceullar carcinoma Deposited 2020-04-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–70（69 aa）
Chain B 2–70（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
7NDX Crystal structure of the human HSP40 DNAJB1-CTDs in complex with a peptide of NudC Deposited 2021-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 157–340（184 aa）
Not recorded EDO 1,2-ETHANEDIOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；298 K；0.1 M of sodium acetate trihydrate and 15% (v/v) of polyethylene glycol 400
Resolution 2.54 Å R-free 0.268
8FE2 Structure of J-PKAc chimera complexed with Aplithianine A Deposited 2022-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–70（69 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) XTI 6-[(6M)-6-(1-methyl-1H-imidazol-5-yl)-2,3-dihydro-4H-1,4-thiazin-4-yl]-9H-purine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；200 mM Lithium sulfate, 100 mM HEPES 7.5, 20% PEG 3350
Resolution 2.34 Å R-free 0.251
8FE2 Structure of J-PKAc chimera complexed with Aplithianine A Deposited 2022-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–70（69 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) XTI 6-[(6M)-6-(1-methyl-1H-imidazol-5-yl)-2,3-dihydro-4H-1,4-thiazin-4-yl]-9H-purine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；200 mM Lithium sulfate, 100 mM HEPES 7.5, 20% PEG 3350
Resolution 2.34 Å R-free 0.251
8FE5 Structure of J-PKAc chimera complexed with Aplithianine B Deposited 2022-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–70（69 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) XTT 6-[(6P)-6-(1-methyl-1H-imidazol-5-yl)-2,3-dihydro-4H-1,4-thiazin-4-yl]-7,9-dihydro-8H-purin-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；200 mM Lithium Sulfate, 100 mM HEPES 7.5, 25% PEG 3350
Resolution 2.51 Å R-free 0.243
8FE5 Structure of J-PKAc chimera complexed with Aplithianine B Deposited 2022-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–70（69 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) XTT 6-[(6P)-6-(1-methyl-1H-imidazol-5-yl)-2,3-dihydro-4H-1,4-thiazin-4-yl]-7,9-dihydro-8H-purin-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；200 mM Lithium Sulfate, 100 mM HEPES 7.5, 25% PEG 3350
Resolution 2.51 Å R-free 0.243
8FEC Structure of J-PKAc chimera complexed with Aplithianine derivative Deposited 2022-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–70（69 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) XU0 6-[(6P)-6-(4-bromo-1-methyl-1H-imidazol-5-yl)-2,3-dihydro-4H-1,4-thiazin-4-yl]-7H-purine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；200 mM Lithium sulfate, 100 mM HEPES 7.5, 25% PEG 3350
Resolution 2.70 Å R-free 0.287
8FEC Structure of J-PKAc chimera complexed with Aplithianine derivative Deposited 2022-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–70（69 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) XU0 6-[(6P)-6-(4-bromo-1-methyl-1H-imidazol-5-yl)-2,3-dihydro-4H-1,4-thiazin-4-yl]-7H-purine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；200 mM Lithium sulfate, 100 mM HEPES 7.5, 25% PEG 3350
Resolution 2.70 Å R-free 0.287
9NFS Structure of J-PKAc chimera in complex with Aplithianine j1 Deposited 2025-02-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–70（69 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1BX1 (4P)-4-[4-(pyrimidin-4-yl)-3,4-dihydro-2H-1,4-thiazin-6-yl]-1H-pyrrolo[2,3-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277.15 K；0.2 M LiCl, 0.1 M hopes, pH 7.6, 25% PEG 3350
Resolution 2.45 Å R-free 0.334
9NFS Structure of J-PKAc chimera in complex with Aplithianine j1 Deposited 2025-02-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–70（69 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1BX1 (4P)-4-[4-(pyrimidin-4-yl)-3,4-dihydro-2H-1,4-thiazin-6-yl]-1H-pyrrolo[2,3-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277.15 K；0.2 M LiCl, 0.1 M hopes, pH 7.6, 25% PEG 3350
Resolution 2.45 Å R-free 0.334

14 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNJB1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–110； UniProt 1–110

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6z5n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6z5n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6z5n
Deposition date deposition_date2020-05-27
Structure title titleDnaJB1 JD-GF
Keywords keywordsMolecular Chaperone, J-domain protein, Hsp40, DnaJ, CHAPERONE; CHAPERONE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.66 Å
Radius of gyration Rg (electron density) rg_electron14.05 Å
Forward intensity I(0) i0240035000.00
Molecular weight molecular_weight122020.0 kDa
Excluded volume excluded_volume149310 ų
Envelope volume envelope_volume27437 ų
Hydration-shell volume shell_volume14687 ų
Envelope diameter envelope_diameter54.1 Å
Shell Rg shell_rg21.72 Å
Envelope Rg envelope_rg16.30 Å
Shape Rg shape_rg14.00 Å
Total Rg total_rg14.45 Å
Total atoms total_atoms16660
Residues n_residues1100
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax49.8 Å
Rg (real space) rg_real14.64 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real2.4000e+08
I(0) uncertainty (real space) i0_real_error2.6400e+06
Rg (reciprocal space) rg_reciprocal14.64 Å
I(0) (reciprocal space) i0_reciprocal240000000.0000
Solution quality estimate total_estimate0.8640
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.7 Å
Skewness Skewness skewness0.320
Kurtosis Kurtosis kurtosis-0.225
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha443100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.970
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id6z5nA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily110 — DnaJ domain
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8. Citations (1)

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9. Files and Curves (10)