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2m6y

The solution structure of the J-domain of human DnaJA1

Method: SOLUTION NMR Dmax: 58.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DnaJ homolog subfamily A member 1

Homo sapiens

UniProt P31689

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 1–67 Fragment：J-domain (UNP residues 1-67) No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 125；Pressure ambient NMR sample composition：1.03 mM [U-13C; U-15N] J-domain of DnaJA1, 20 mM MES, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 50 uM DSS, 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 2M6Y Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LO1 NMR structure of the protein BC008182, a DNAJ-like domain from Homo sapiens Deposited 2012-01-09 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–70（70 aa） Fragment：J domain residues 1-70
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.080；Pressure ambient
NMR sample composition 1.2 mM [U-98% 13C; U-98% 15N] protein, 20 mM sodium phosphate, 5 mM sodium azide, 50 mM sodium chloride, 95 % H2O, 5 % D2O, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6E8M Legionella Longbeachae LeSH (Llo2327) bound to the human DnaJ-A1 pTyr381 peptide Deposited 2018-07-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 375–387（13 aa）
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；296 K；PEG3000, malic acid, Tris-HCl
Resolution 1.61 Å R-free 0.212

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNJA1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 11–77； UniProt 1–67

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 2m6y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2m6y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2m6y
Deposition date deposition_date2013-04-14
Structure title titleThe solution structure of the J-domain of human DnaJA1
Keywords keywordsprotein, CHAPERONE, Structural Genomics, PSI-Biology, Northeast Structural Genomics Consortium, NESG; 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_guinier14.46 Å
Radius of gyration Rg (electron density) rg_electron13.98 Å
Forward intensity I(0) i0482737000.00
Molecular weight molecular_weight181530.0 kDa
Excluded volume excluded_volume225710 ų
Envelope volume envelope_volume34648 ų
Hydration-shell volume shell_volume16435 ų
Envelope diameter envelope_diameter62.3 Å
Shell Rg shell_rg23.99 Å
Envelope Rg envelope_rg18.94 Å
Shape Rg shape_rg13.92 Å
Total Rg total_rg14.46 Å
Total atoms total_atoms25380
Residues n_residues1540
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 dmax58.0 Å
Rg (real space) rg_real14.46 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real4.8270e+08
I(0) uncertainty (real space) i0_real_error6.1200e+06
Rg (reciprocal space) rg_reciprocal14.46 Å
I(0) (reciprocal space) i0_reciprocal482700000.0000
Solution quality estimate total_estimate0.7743
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.2 Å
Skewness Skewness skewness0.325
Kurtosis Kurtosis kurtosis-0.108
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha158500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.473; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.642; Smooth: 1.000
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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2m6ya1
Class classa — All alpha proteins
Fold Fold folda.2 — Long alpha-hairpin
Superfamily Superfamily superfamilya.2.3 — Chaperone J-domain
Family Family familya.2.3.0 — automated matches
Domain ID domain_idd2m6ya2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2m6yA01
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)