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8hae

Cryo-EM structure of HACE1 dimer

Method: ELECTRON MICROSCOPY Dmax: 162.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase HACE1

Homo sapiens

UniProt Q8IYU2

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–909 Chain B； UniProt 1–909 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.55 Å

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 8HAE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8H8X Cryo-EM structure of HACE1 monomer Deposited 2022-10-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–909（909 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；gel filtration
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
8PWL Cryo-EM structure of a full-length HACE1 dimer Deposited 2023-07-20 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–909（909 aa）
Chain B 1–909（909 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.73 Å
8Q0N HACE1 in complex with RAC1 Q61L Deposited 2023-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–909（888 aa）
Mutation：deletion 1-21 04E iodoacetic acid × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HACE1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–909； UniProt 1–909 Author chain B； PDBConstruct 1–909； UniProt 1–909

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 8hae

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8hae
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8hae
Deposition date deposition_date2022-10-26
Structure title titleCryo-EM structure of HACE1 dimer
Keywords keywordsE3 ubiquitin ligase, tumor suppressor, Post-translational modifier, Protein degradation, ANTITUMOR PROTEIN; ANTITUMOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier51.85 Å
Radius of gyration Rg (electron density) rg_electron51.75 Å
Forward intensity I(0) i0532396000.00
Molecular weight molecular_weight191230.0 kDa
Excluded volume excluded_volume238840 ų
Envelope volume envelope_volume394880 ų
Hydration-shell volume shell_volume62672 ų
Envelope diameter envelope_diameter170.0 Å
Shell Rg shell_rg58.19 Å
Envelope Rg envelope_rg49.10 Å
Shape Rg shape_rg51.74 Å
Total Rg total_rg52.02 Å
Total atoms total_atoms26698
Residues n_residues1690
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 dmax162.5 Å
Rg (real space) rg_real51.77 Å
Rg uncertainty (real space) rg_real_error1.61 Å
I(0) (real space) i0_real5.3240e+08
I(0) uncertainty (real space) i0_real_error1.1400e+07
Rg (reciprocal space) rg_reciprocal51.89 Å
I(0) (reciprocal space) i0_reciprocal532500000.0000
Solution quality estimate total_estimate0.8734
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary81.2 Å
Skewness Skewness skewness0.083
Kurtosis Kurtosis kurtosis-0.783
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28720000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.502
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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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8. Citations (1)

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9. Files and Curves (10)