3agy

Crystal structure of human Hsp40 Hdj1 peptide-binding domain complexed with a C-terminal peptide of Hsp70

Method: X-RAY DIFFRACTION Dmax: 97.7 Å Quality: GOOD

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 161–340 Chain B; UniProt 161–340 Fragment:UNP residues 161-340 peptide of Heat shock cognate 71 kDa protein × 3 (P11142) 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

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.

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 2–181; UniProt 161–340 Author chain B; PDBConstruct 2–181; UniProt 161–340

peptide of Heat shock cognate 71 kDa protein

OrganismNot specified

UniProt P11142

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 639–646 Chain D; UniProt 639–646 Chain F; UniProt 639–646 Fragment:UNP residues 639-646 DnaJ homolog subfamily B member 1 × 2 (P25685) 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

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.

37 other PDB entries and 66 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HSP7C_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–8; UniProt 639–646 Author chain D; PDBConstruct 1–8; UniProt 639–646 Author chain F; PDBConstruct 1–8; UniProt 639–646

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 3agy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3agy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3agy
Deposition date deposition_date2010-04-12
Structure title titleCrystal structure of human Hsp40 Hdj1 peptide-binding domain complexed with a C-terminal peptide of Hsp70
Keywords keywordschaperone; CHAPERONE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.88
Radius of gyration Rg (electron density) rg_electron30.89
Forward intensity I(0) i027415100.00
Molecular weight molecular_weight42079.0 kDa
Excluded volume excluded_volume53331 ų
Envelope volume envelope_volume77490 ų
Hydration-shell volume shell_volume21682 ų
Envelope diameter envelope_diameter101.9
Shell Rg shell_rg36.86
Envelope Rg envelope_rg29.86
Shape Rg shape_rg30.87
Total Rg total_rg31.56
Total atoms total_atoms2958
Residues n_residues373
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax97.7
Rg (real space) rg_real31.82
Rg uncertainty (real space) rg_real_error1.11
I(0) (real space) i0_real2.7420e+07
I(0) uncertainty (real space) i0_real_error4.7820e+05
Rg (reciprocal space) rg_reciprocal31.85
I(0) (reciprocal space) i0_reciprocal27420000.0000
Solution quality estimate total_estimate0.8639
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.9
Skewness Skewness skewness0.013
Kurtosis Kurtosis kurtosis-0.846
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1740000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.905; Smooth: 0.873

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3agyA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily20 — Urease metallochaperone UreE, N-terminal domain
Domain ID domain_id3agyA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily20 — Urease metallochaperone UreE, N-terminal domain
Domain ID domain_id3agyB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily20 — Urease metallochaperone UreE, N-terminal domain
Domain ID domain_id3agyB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily20 — Urease metallochaperone UreE, N-terminal domain

8. Citations (1)

9. Files and Curves (10)