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9z0e

Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc

Method: ELECTRON MICROSCOPY D_max: 142.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z0e
deposition_date	2025-10-31
title	Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc
keywords	MEMBRANE PROTEIN, Hrd1 ubiquitin ligase, Hrd3, MSP1D1 nanodisc; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	42.40 Å
rg_electron	41.98 Å
i0	246729000.00
molecular_weight	136020.0 kDa
excluded_volume	173430 Å³
envelope_volume	256230 Å³
shell_volume	51675 Å³
envelope_diameter	141.1 Å
shell_rg	46.53 Å
envelope_rg	40.69 Å
shape_rg	42.00 Å
total_rg	42.19 Å
total_atoms	9605
n_residues	1163
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	142.1 Å
rg_real	42.45 Å
rg_real_error	1.68 Å
i0_real	2.4670e+08
i0_real_error	4.9170e+06
rg_reciprocal	42.40 Å
i0_reciprocal	246700000.0000
total_estimate	0.8241
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.1 Å
skewness	0.293
kurtosis	-0.584
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	26010000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	ERAD-associated E3 ubiquitin-protein ligase HRD1
formula_weight	40129.1 kDa
ec_number	2.3.2.27
mutation	I91C
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,C
atom_count	9605

MVPENRRKQLAIFVVVTYLLTFYCVYSATKTSVSFLQVTLKLNEGFNLMVLSIFILLNSTLLWQLLTKLLFGELRLIEHEHIFERLPFTICNTLFMSSLFHERYFFTVAFFGLLLLYLKVFHWILKDRLEALLQSINDSTTMKTLIFSRFSFNLVLLAVVDYQIITRCISSIYTNQKSDIESTSLYLIQVMEFTMLLIDLLNLFLQTCLNFWEFYRSQQSLSNENNHIVHGDPTDENTVESDQSQPVLNDDDDDDDDDRQFTGLEGKFMYEKAIDVFTRFLKTALHLSMLIPFRMPMMLLKDVVWDILALYQSGTSLWKIWRNNKQGSGGASGGSGDYKDDDDK

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Saccharomyces cerevisiae

Entity 2 polymer

description	ERAD-associated E3 ubiquitin-protein ligase component HRD3
formula_weight	93787.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MITLLLYLCVICNAIVLIRADSIADPWPEARHLLNTIAKSRDPMKEAAMEPNADEFVGFYVPMDYSPRNEEKNYQSIWQNEITDSQRHIYELLVQSSEQFNNSEATYTLSQIHLWSQYNFPHNMTLAHKYLEKFNDLTHFTNHSAIFDLAVMYATGGCASGNDQTVIPQDSAKALLYYQRAAQLGNLKAKQVLAYKYYSGFNVPRNFHKSLVLYRDIAEQLRKSYSRDEWDIVFPYWESYNVRISDFESGLLGKGLNSVPSSTVRKRTTRPDIGSPFIAQVNGVQMTLQIEPMGRFAFNGNDGNINGDEDDEDASERRIIRIYYAALNDYKGTYSQSRNCERAKNLLELTYKEFQPHVDNLDPLQVFYYVRCLQLLGHMYFTGEGSSKPNIHMAEEILTTSLEISRRAQGPIGRACIDLGLINQYITNNISQAISYYMKAMKTQANNGIVEFQLSKLATSFPEEKIGDPFNLMETAYLNGFIPAIYEFAVMIESGMNSKSSVENTAYLFKTFVDKNEAIMAPKLRTAFAALINDRSEVALWAYSQLAEQGYETAQVSAAYLMYQLPYEFEDPPRTTDQRKTLAISYYTRAFKQGNIDAGVVAGDIYFQMQNYSKAMALYQGAALKYSIQAIWNLGYMHEHGLGVNRDFHLAKRYYDQVSEHDHRFYLASKLSVLKLHLKSWLTWITREKVNYWKPSSPLNPNEDTQHSKTSWYKQLTKILQRMRHKEDSDKAAEDSHKHRTVVQNGANHRGDDQEEASEILGFQMEDGGGENLYFQSGGGMDERTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Saccharomyces cerevisiae

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	3.70 Å
resolution_method	—
num_particles	126359

fit	/app/data/saxs_computation/z0/9z0e/9z0e.fit
pddf	/app/data/pr_computation/z0/9z0e/9z0e.pr.out
profile	/app/data/saxs_computation/z0/9z0e/9z0e.dat

Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)