SAXSdb — 9ua3

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1. Structure Basics

entry_id	9ua3
deposition_date	2025-03-31
title	Cryo-EM structure of neddylated CUL2-RBX1-FEM1C-ELOB-ELOC
keywords	E3 ubiquitin ligase, ARG/C-degron, degradation, 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	52.70 Å
rg_electron	52.56 Å
i0	931992000.00
molecular_weight	255340.0 kDa
excluded_volume	320540 Å³
envelope_volume	470870 Å³
shell_volume	77707 Å³
envelope_diameter	192.1 Å
shell_rg	52.72 Å
envelope_rg	51.43 Å
shape_rg	52.59 Å
total_rg	52.49 Å
total_atoms	17924
n_residues	2244
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	183.2 Å
rg_real	55.20 Å
rg_real_error	0.89 Å
i0_real	9.3510e+08
i0_real_error	1.4310e+07
rg_reciprocal	52.61 Å
i0_reciprocal	931700000.0000
total_estimate	0.6668
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	61.1 Å
skewness	0.501
kurtosis	-0.103
angular_range	— – 0.1500 Å⁻¹
current_alpha	1.1740
highest_alpha	43070000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 0.864; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.426

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Protein fem-1 homolog C
formula_weight	68767.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	17924

MDLKTAVFNAARDGKLRLLTKLLASKSKEEVSSLISEKTNGATPLLMAARYGHLDMVEFLLEQCSASIEVGGSVNFDGETIEGAPPLWAASAAGHLKVVQSLLNHGASVNNTTLTNSTPLRAACFDGHLEIVKYLVEHKADLEVSNRHGHTCLMISCYKGHKEIAQYLLEKGADVNRKSVKGNTALHDCAESGSLDIMKMLLMYCAKMEKDGYGMTPLLSASVTGHTNIVDFLTHHAQTSKTERINALELLGATFVDKKRDLLGALKYWKKAMNMRYSDRTNIISKPVPQTLIMAYDYAKEVNSAEELEGLIADPDEMRMQALLIRERILGPSHPDTSYYIRYRGAVYADSGNFKRCINLWKYALDMQQSNLDPLSPMTASSLLSFAELFSFMLQDRAKGLLGTTVTFDDLMGILCKSVLEIERAIKQTQCPADPLQLNKALSIILHLICLLEKVPCTLEQDHFKKQTIYRFLKLHPRGKNNFSPLHLAVDKNTTCVGRYPVCKFPSLQVTAILIECGADVNVRDSDDNSPLHIAALNNHPDIMNLLIKSGAHFDATNLHKQTASDLLDEKEIAKNLIQPINHTTLQCLAARVIVNHRIYYKGHIPEKLETFVSLHR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Cullin-2
formula_weight	87068.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

TSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTEADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Elongin-B
formula_weight	13147.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	Elongin-C
formula_weight	10843.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 polymer

description	ALA-ARG-ALA-ARG
formula_weight	474.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,J

ARAR

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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	—

resolution	3.280 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.28 Å
resolution_method	—
num_particles	673233

fit	/app/data/saxs_computation/ua/9ua3/9ua3.fit
pddf	/app/data/pr_computation/ua/9ua3/9ua3.pr.out
profile	/app/data/saxs_computation/ua/9ua3/9ua3.dat

Cryo-EM structure of neddylated CUL2-RBX1-FEM1C-ELOB-ELOC

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

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)