SAXSdb — 7ndx

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DnaJ homolog subfamily B member 1

Homo sapiens

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 157–340	Not recorded	Nuclear migration protein nudC × 2 （Q9Y266） 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

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 7NDX	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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 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 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
6Z5N DnaJB1 JD-GF Deposited 2020-05-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–110（110 aa）	Not recorded	No recorded non-water small molecule	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
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 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 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 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 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 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 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 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 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 1–184； UniProt 157–340

Nuclear migration protein nudC

Homo sapiens

UniProt Q9Y266

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 100–141	Not recorded	DnaJ homolog subfamily B member 1 × 2 （P25685） 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

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 7NDX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QOR Crystal structure of human nuclear migration protein NudC Deposited 2011-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 158–274（117 aa） Fragment：residues 158-274	Mutation：E236A, K129A Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；296 K；25% PEG 3350, 0.2M sodium acetate, 0.1M lithium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 1.75 Å R-free 0.202
3QOR Crystal structure of human nuclear migration protein NudC Deposited 2011-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 158–274（117 aa） Fragment：residues 158-274	Mutation：E236A, K129A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；296 K；25% PEG 3350, 0.2M sodium acetate, 0.1M lithium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 1.75 Å R-free 0.202
3QOR Crystal structure of human nuclear migration protein NudC Deposited 2011-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 158–274（117 aa） Fragment：residues 158-274	Mutation：E236A, K129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；296 K；25% PEG 3350, 0.2M sodium acetate, 0.1M lithium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 1.75 Å R-free 0.202
3QOR Crystal structure of human nuclear migration protein NudC Deposited 2011-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 158–274（117 aa） Fragment：residues 158-274	Mutation：E236A, K129A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；296 K；25% PEG 3350, 0.2M sodium acetate, 0.1M lithium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 1.75 Å R-free 0.202
3QOR Crystal structure of human nuclear migration protein NudC Deposited 2011-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 158–274（117 aa） Fragment：residues 158-274	Mutation：E236A, K129A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；296 K；25% PEG 3350, 0.2M sodium acetate, 0.1M lithium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 1.75 Å R-free 0.202

1 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NUDC_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–42； UniProt 100–141

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7ndx
Deposition date deposition_date	2021-02-02
Structure title title	Crystal structure of the human HSP40 DNAJB1-CTDs in complex with a peptide of NudC
Keywords keywords	Chaperones, Protein Complex, CHAPERONE; CHAPERONE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.37 Å
Radius of gyration Rg (electron density) rg_electron	24.28 Å
Forward intensity I(0) i0	7289730.00
Molecular weight molecular_weight	20576.0 kDa
Excluded volume excluded_volume	26150 Å³
Envelope volume envelope_volume	35739 Å³
Hydration-shell volume shell_volume	14327 Å³
Envelope diameter envelope_diameter	97.9 Å
Shell Rg shell_rg	27.19 Å
Envelope Rg envelope_rg	25.16 Å
Shape Rg shape_rg	24.29 Å
Total Rg total_rg	24.73 Å
Total atoms total_atoms	2962
Residues n_residues	181
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	95.4 Å
Rg (real space) rg_real	24.92 Å
Rg uncertainty (real space) rg_real_error	1.24 Å
I(0) (real space) i0_real	7.2900e+06
I(0) uncertainty (real space) i0_real_error	1.2880e+05
Rg (reciprocal space) rg_reciprocal	24.79 Å
I(0) (reciprocal space) i0_reciprocal	7289000.0000
Solution quality estimate total_estimate	0.7018
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.7 Å
Skewness Skewness skewness	0.716
Kurtosis Kurtosis kurtosis	0.029
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1329000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.355; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.066; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DnaJ homolog subfamily B member 1
Molecular weight formula_weight	20894.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2984

RKKQDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKKGWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGCTVNVPTLDGRTIPVVFKDVIRPGMRRKVPGEGLPLPKTPEKRGDLIIEFEVIFPERIPQTSRTVLEQVLPI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nuclear migration protein nudC
Molecular weight formula_weight	4668.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SGPQIKELTDEEAERLQLEIDQKKDAENHEAQLKNGSLDSPG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7ndxA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

Domain ID domain_id	7ndxA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	41.300 Å
Unit-cell length b length_b	128.264 Å
Unit-cell length c length_c	135.213 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	2.541 Å
Low-resolution limit resolution_low	46.530 Å
R factor r_factor	—
R_work r_work	0.2328
R_free r_free	0.2681

fit	/app/data/saxs_computation/nd/7ndx/7ndx.fit
pddf	/app/data/pr_computation/nd/7ndx/7ndx.pr.out
profile	/app/data/saxs_computation/nd/7ndx/7ndx.dat

Crystal structure of the human HSP40 DNAJB1-CTDs in complex with a peptide of NudC

1. Protein Identity and Related Structures Protein Identity & Related Structures

DnaJ homolog subfamily B member 1

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear migration protein nudC

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)