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5v7v

Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3

Method: ELECTRON MICROSCOPY Dmax: 96.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ERAD-associated E3 ubiquitin-protein ligase component HRD3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q05787

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–767 Fragment：UNP residues 1-767 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 5V7V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VJY Cryo-EM structure of Hrd1/Hrd3 monomer Deposited 2020-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–767（767 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6VJZ CryoEM structure of Hrd1-Usa1/Der1/Hrd3 complex of the expected topology Deposited 2020-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–767（767 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6VK0 CryoEM structure of Hrd1-Usa1/Der1/Hrd3 of the flipped topology Deposited 2020-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–767（767 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6VK1 CryoEM structure of Hrd1/Hrd3 part from Hrd1-Usa1/Der1/Hrd3 complex Deposited 2020-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–767（767 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9Z0E Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc Deposited 2025-10-31 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–767（767 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name HRD3_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–767； UniProt 1–767

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 5v7v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5v7v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5v7v
Deposition date deposition_date2017-03-20
Structure title titleCryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3
Keywords keywordsHrd3 ERAD, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.06 Å
Radius of gyration Rg (electron density) rg_electron29.36 Å
Forward intensity I(0) i084213800.00
Molecular weight molecular_weight72344.0 kDa
Excluded volume excluded_volume90632 ų
Envelope volume envelope_volume122900 ų
Hydration-shell volume shell_volume35388 ų
Envelope diameter envelope_diameter104.5 Å
Shell Rg shell_rg36.07 Å
Envelope Rg envelope_rg29.40 Å
Shape Rg shape_rg29.35 Å
Total Rg total_rg30.06 Å
Total atoms total_atoms10035
Residues n_residues613
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 dmax96.1 Å
Rg (real space) rg_real29.97 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real8.4210e+07
I(0) uncertainty (real space) i0_real_error1.4330e+06
Rg (reciprocal space) rg_reciprocal30.01 Å
I(0) (reciprocal space) i0_reciprocal84220000.0000
Solution quality estimate total_estimate0.9072
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.3 Å
Skewness Skewness skewness0.194
Kurtosis Kurtosis kurtosis-0.552
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20780000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.980
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)