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9r85

Cryo-EM structure of the E3 ligase HECTD3 conjugated to ubiquitin

Method: ELECTRON MICROSCOPY D_max: 111.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r85
deposition_date	2025-05-15
title	Cryo-EM structure of the E3 ligase HECTD3 conjugated to ubiquitin
keywords	E3-ligase, ubiquitin, ubiquitination, HECT-ligase, LIGASE; LIGASE
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	34.05 Å
rg_electron	33.46 Å
i0	155480000.00
molecular_weight	100330.0 kDa
excluded_volume	126020 Å³
envelope_volume	169990 Å³
shell_volume	43090 Å³
envelope_diameter	118.1 Å
shell_rg	39.44 Å
envelope_rg	33.10 Å
shape_rg	33.45 Å
total_rg	34.01 Å
total_atoms	14072
n_residues	885
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	111.9 Å
rg_real	34.02 Å
rg_real_error	0.90 Å
i0_real	1.5550e+08
i0_real_error	2.6030e+06
rg_reciprocal	34.04 Å
i0_reciprocal	155500000.0000
total_estimate	0.8956
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	41.4 Å
skewness	0.312
kurtosis	-0.284
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	24800000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.953

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Ubiquitin
formula_weight	8519.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	14072

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	E3 ubiquitin-protein ligase HECTD3
formula_weight	97441.1 kDa
ec_number	2.3.2.26
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

GPGMAGPGPGAVLESPRQLLGRVRFLAEAARSLRAGRPLPAALAFVPREVLYKLYKDPAGPSRVLLPVWEAEGLGLRVGAAGPAPGTGSGPLRAARDSIELRRGACVRTTGEELCNGHGLWVKLTKEQLAEHLGDCGLQEGWLLVCRPAEGGARLVPIDTPNHLQRQQQLFGVDYRPVLRWEQVVDLTYSHRLGSRPQPAEAYAEAVQRLLYVPPTWTYECDEDLIHFLYDHLGKEDENLGSVKQYVESIDVSSYTEEFNVSCLTDSNADTYWESDGSQCQHWVRLTMKKGTIVKKLLLTVDTTDDNFMPKRVVVYGGEGDNLKKLSDVSIDETLIGDVCVLEDMTVHLPIIEIRIVECRDDGIDVRLRGVKIKSSRQRELGLNADLFQPTSLVRYPRLEGTDPEVLYRRAVLLQRFIKILDSVLHHLVPAWDHTLGTFSEIKQVKQFLLLSRQRPGLVAQCLRDSESSKPSFMPRLYINRRLAMEHRACPSRDPACKNAVFTQVYEGLKPSDKYEKPLDYRWPMRYDQWWECKFIAEGIIDQGGGFRDSLADMSEELCPSSADTPVPLPFFVRTANQGNGTGEARDMYVPNPSCRDFAKYEWIGQLMGAALRGKEFLVLALPGFVWKQLSGEEVSWSKDFPAVDSVLVKLLEVMEGMDKETFEFKFGKELTFTTVLSDQQVVELIPGGAGIVVGYGDRSRFIQLVQKARLEESKEQVAAMQAGLLKVVPQAVLDLLTWQELEKKVCGDPEVTVDALRKLTRFEDFEPSDSRVQYFWEALNNFTNEDRSRFLRFVTGRSRLPARIYIYPDKLGYETTDALPESSTCSSTLFLPHYASAKVCEEKLRYAAYNCVAIDTDMSPWEE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 non-polymer

description	prop-2-en-1-amine
formula_weight	57.1 kDa
src_method	syn
entity_count	1

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6. Citations (2)

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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	3.04 Å
resolution_method	—
num_particles	342589

fit	/app/data/saxs_computation/r8/9r85/9r85.fit
pddf	/app/data/pr_computation/r8/9r85/9r85.pr.out
profile	/app/data/saxs_computation/r8/9r85/9r85.dat

Cryo-EM structure of the E3 ligase HECTD3 conjugated to ubiquitin

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)