SAXSdb — 6vk1

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ERAD-associated E3 ubiquitin-protein ligase HRD1

Saccharomyces cerevisiae

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–480	Not recorded	ERAD-associated E3 ubiquitin-protein ligase component HRD3 × 1 （Q05787）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 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 6VK1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5V6P CryoEM structure of the ERAD-associated E3 ubiquitin-protein ligase HRD1 Deposited 2017-03-17	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 1–407（407 aa） Fragment：UNP residues 1-407 Chain B 1–407（407 aa） Fragment：UNP residues 1-407	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6VJY Cryo-EM structure of Hrd1/Hrd3 monomer Deposited 2020-01-18	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–430（430 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 oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–480（480 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 oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–480（480 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
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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–326（326 aa） Chain C 1–326（326 aa）	Mutation：I91C Mutation：I91C	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	HRD1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–480； UniProt 1–480

ERAD-associated E3 ubiquitin-protein ligase component HRD3

Saccharomyces cerevisiae

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	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–767	Not recorded	ERAD-associated E3 ubiquitin-protein ligase HRD1 × 1 （Q08109）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 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 6VK1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5V7V Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3 Deposited 2017-03-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–767（767 aa） Fragment：UNP residues 1-767	Not recorded	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
6VJY Cryo-EM structure of Hrd1/Hrd3 monomer Deposited 2020-01-18	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 oligomeric state 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 oligomeric state 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
9Z0E Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc Deposited 2025-10-31	Different oligomeric state Different experimental conditions 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	2
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6vk1
Deposition date deposition_date	2020-01-18
Structure title title	CryoEM structure of Hrd1/Hrd3 part from Hrd1-Usa1/Der1/Hrd3 complex
Keywords keywords	retro-translocation, ERAD, protein degradation, ubiquitination, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	40.43 Å
Radius of gyration Rg (electron density) rg_electron	40.59 Å
Forward intensity I(0) i0	147952000.00
Molecular weight molecular_weight	102760.0 kDa
Excluded volume excluded_volume	130340 Å³
Envelope volume envelope_volume	192460 Å³
Hydration-shell volume shell_volume	41602 Å³
Envelope diameter envelope_diameter	143.6 Å
Shell Rg shell_rg	43.63 Å
Envelope Rg envelope_rg	39.95 Å
Shape Rg shape_rg	40.59 Å
Total Rg total_rg	40.81 Å
Total atoms total_atoms	7259
Residues n_residues	882
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	137.4 Å
Rg (real space) rg_real	40.69 Å
Rg uncertainty (real space) rg_real_error	1.36 Å
I(0) (real space) i0_real	1.4800e+08
I(0) uncertainty (real space) i0_real_error	2.5540e+06
Rg (reciprocal space) rg_reciprocal	40.43 Å
I(0) (reciprocal space) i0_reciprocal	147900000.0000
Solution quality estimate total_estimate	0.8412
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.8 Å
Skewness Skewness skewness	0.486
Kurtosis Kurtosis kurtosis	-0.388
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15240000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.761; Smooth: 0.666

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	ERAD-associated E3 ubiquitin-protein ligase HRD1
Molecular weight formula_weight	55638.8 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	7259

MVPENRRKQLAIFVVVTYLLTFYCVYSATKTSVSFLQVTLKLNEGFNLMVLSIFILLNSTLLWQLLTKLLFGELRLIEHEHIFERLPFTIINTLFMSSLFHERYFFTVAFFGLLLLYLKVFHWILKDRLEALLQSINDSTTMKTLIFSRFSFNLVLLAVVDYQIITRCISSIYTNQKSDIESTSLYLIQVMEFTMLLIDLLNLFLQTCLNFWEFYRSQQSLSNENNHIVHGDPTDENTVESDQSQPVLNDDDDDDDDDRQFTGLEGKFMYEKAIDVFTRFLKTALHLSMLIPFRMPMMLLKDVVWDILALYQSGTSLWKIWRNNKQLDDTLVTVTVEQLQNSANDDNICIICMDELIHSPNQQTWKNKNKKPKRLPCGHILHLSCLKNWMERSQTCPICRLPVFDEKGNVVQTTFTSNSDITTQTTVTDSTGIATDQQGFANEVDLLPTRTTSPDIRIVPTQNIDTLAMRTRSTSTPSPT

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	ERAD-associated E3 ubiquitin-protein ligase component HRD3
Molecular weight formula_weight	88239.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MITLLLYLCVICNAIVLIRADSIADPWPEARHLLNTIAKSRDPMKEAAMEPNADEFVGFYVPMDYSPRNEEKNYQSIWQNEITDSQRHIYELLVQSSEQFNNSEATYTLSQIHLWSQYNFPHNMTLAHKYLEKFNDLTHFTNHSAIFDLAVMYATGGCASGNDQTVIPQDSAKALLYYQRAAQLGNLKAKQVLAYKYYSGFNVPRNFHKSLVLYRDIAEQLRKSYSRDEWDIVFPYWESYNVRISDFESGLLGKGLNSVPSSTVRKRTTRPDIGSPFIAQVNGVQMTLQIEPMGRFAFNGNDGNINGDEDDEDASERRIIRIYYAALNDYKGTYSQSRNCERAKNLLELTYKEFQPHVDNLDPLQVFYYVRCLQLLGHMYFTGEGSSKPNIHMAEEILTTSLEISRRAQGPIGRACIDLGLINQYITNNISQAISYYMKAMKTQANNGIVEFQLSKLATSFPEEKIGDPFNLMETAYLNGFIPAIYEFAVMIESGMNSKSSVENTAYLFKTFVDKNEAIMAPKLRTAFAALINDRSEVALWAYSQLAEQGYETAQVSAAYLMYQLPYEFEDPPRTTDQRKTLAISYYTRAFKQGNIDAGVVAGDIYFQMQNYSKAMALYQGAALKYSIQAIWNLGYMHEHGLGVNRDFHLAKRYYDQVSEHDHRFYLASKLSVLKLHLKSWLTWITREKVNYWKPSSPLNPNEDTQHSKTSWYKQLTKILQRMRHKEDSDKAAEDSHKHRTVVQNGANHRGDDQEEASEILGFQMED

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	425035

fit	/app/data/saxs_computation/vk/6vk1/6vk1.fit
pddf	/app/data/pr_computation/vk/6vk1/6vk1.pr.out
profile	/app/data/saxs_computation/vk/6vk1/6vk1.dat

CryoEM structure of Hrd1/Hrd3 part from Hrd1-Usa1/Der1/Hrd3 complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

ERAD-associated E3 ubiquitin-protein ligase HRD1

State in the Current Structure

Other States of the Same Protein in the Database

ERAD-associated E3 ubiquitin-protein ligase component HRD3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)