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8h8x

Cryo-EM structure of HACE1 monomer

Method: ELECTRON MICROSCOPY Dmax: 153.9 Å Quality: REASONABLE
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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–909 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8；gel filtration cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.92 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 8H8X Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8HAE Cryo-EM structure of HACE1 dimer Deposited 2022-10-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions 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 4.55 Å
8PWL Cryo-EM structure of a full-length HACE1 dimer Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions 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 experimental conditions 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

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 8h8x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8h8x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8h8x
Deposition date deposition_date2022-10-24
Structure title titleCryo-EM structure of HACE1 monomer
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_guinier43.62 Å
Radius of gyration Rg (electron density) rg_electron43.92 Å
Forward intensity I(0) i0142857000.00
Molecular weight molecular_weight96143.0 kDa
Excluded volume excluded_volume120060 ų
Envelope volume envelope_volume193090 ų
Hydration-shell volume shell_volume39342 ų
Envelope diameter envelope_diameter151.6 Å
Shell Rg shell_rg44.63 Å
Envelope Rg envelope_rg43.21 Å
Shape Rg shape_rg43.89 Å
Total Rg total_rg44.08 Å
Total atoms total_atoms13418
Residues n_residues850
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 dmax153.9 Å
Rg (real space) rg_real44.05 Å
Rg uncertainty (real space) rg_real_error2.03 Å
I(0) (real space) i0_real1.4290e+08
I(0) uncertainty (real space) i0_real_error2.8370e+06
Rg (reciprocal space) rg_reciprocal43.62 Å
I(0) (reciprocal space) i0_reciprocal142800000.0000
Solution quality estimate total_estimate0.5256
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary149.6 Å
Skewness Skewness skewness0.472
Kurtosis Kurtosis kurtosis-0.506
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9254000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 0.005; Positv: 1.000; Valcen: 0.601; Smooth: 0.000
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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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8. Citations (1)

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9. Files and Curves (10)