SAXSdb — 9t32

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1. Structure Basics

entry_id	9t32
deposition_date	2025-10-24
last_revision	2025-12-03
title	The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11
keywords	PROTAC, homoPROTAC, dimerizer, CM11, VHL, von Hippel-Lindau, Cullin 2, RING, E3, ligase, targeted protein degradation; 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	67.89 Å
rg_electron	67.67 Å
i0	841488000.00
molecular_weight	248900.0 kDa
excluded_volume	313020 Å³
envelope_volume	528580 Å³
shell_volume	67573 Å³
envelope_diameter	199.7 Å
shell_rg	65.87 Å
envelope_rg	62.69 Å
shape_rg	67.66 Å
total_rg	67.67 Å
total_atoms	34854
n_residues	2136
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	187.9 Å
rg_real	67.77 Å
rg_real_error	1.76 Å
i0_real	8.4150e+08
i0_real_error	1.8140e+07
rg_reciprocal	68.10 Å
i0_reciprocal	841900000.0000
total_estimate	0.6228
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	89.9 Å
skewness	-0.053
kurtosis	-0.840
angular_range	— – 0.1150 Å⁻¹
current_alpha	0.0000
highest_alpha	17170000.0000
n_real_points	24
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.997; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Elongin-B
formula_weight	11619.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,F
atom_count	34854

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Elongin-C
formula_weight	10740.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,J

MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Cullin-2
formula_weight	76636.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,I

KPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTEADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	E3 ubiquitin-protein ligase RBX1, N-terminally processed
formula_weight	10526.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	R,S

KRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 polymer

description	von Hippel-Lindau disease tumor suppressor
formula_weight	16335.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,C

VLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 6 non-polymer

description	;(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[2-[2-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ;
formula_weight	1179.4 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	6.90 Å
resolution_method	—
num_particles	68789

fit	/app/data/saxs_computation/t3/9t32/9t32.fit
pddf	/app/data/pr_computation/t3/9t32/9t32.pr.out
profile	/app/data/saxs_computation/t3/9t32/9t32.dat

The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)