SAXSdb — 9sdy

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1. Structure Basics

entry_id	9sdy
deposition_date	2025-08-15
title	Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2
keywords	Complex, 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	45.12 Å
rg_electron	45.32 Å
i0	256329000.00
molecular_weight	129420.0 kDa
excluded_volume	161350 Å³
envelope_volume	254650 Å³
shell_volume	49658 Å³
envelope_diameter	152.7 Å
shell_rg	46.15 Å
envelope_rg	44.54 Å
shape_rg	45.37 Å
total_rg	45.21 Å
total_atoms	9073
n_residues	1172
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	147.7 Å
rg_real	45.16 Å
rg_real_error	1.30 Å
i0_real	2.5630e+08
i0_real_error	4.4250e+06
rg_reciprocal	45.12 Å
i0_reciprocal	256300000.0000
total_estimate	0.8960
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	50.6 Å
skewness	0.211
kurtosis	-0.708
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	14160000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.855

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	L3A2-1
formula_weight	17854.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G
atom_count	9073

MVAASSRLMKELEEIRKAGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFAKNAEEFTKKYGEKRPVD

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 polymer

description	RING-box protein 2
formula_weight	12697.4 kDa
ec_number	2.3.2.27,2.3.2.32
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

MADVEDGEETCALASHSGSSGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 3 polymer

description	Cullin-5
formula_weight	91085.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MATSNLLKNKGSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAKIHQALKEDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMGKQGSNKKSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGVRESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKEEEKRALRYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNGIEPMLKDLEEHIISAGLADMVAAAETITTDSEKYVEQLLTLFNRFSKLVKEAFQDDPRFLTARDKAYKAVVNDATIFKLELPLKQKGVGLKTQPESKCPELLANYCDMLLRKTPLSKKLTSEEIEAKLKEVLLVLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWSRSSEKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 4 polymer

description	E3 ubiquitin-protein ligase ARIH2
formula_weight	57893.8 kDa
ec_number	2.3.2.31
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MSVDMNSQGSDSNEEDYDPNCEEEEEEEEDDPGDIEDYYVGVASDVEQQGADAFDPEEYQFTCLTYKESEGALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEARVQPNPSKHVPTSHPPHHCAVCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVGVSCMAQDCPLRTPEDFVFPLLPNEELREKYRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQAREALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAKCRYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIENLSWKVERADSYDRGDLENQMHIAEQRRRTLLKDFHDT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	7

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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	3.060 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.06 Å
resolution_method	—
num_particles	191502

fit	/app/data/saxs_computation/sd/9sdy/9sdy.fit
pddf	/app/data/pr_computation/sd/9sdy/9sdy.pr.out
profile	/app/data/saxs_computation/sd/9sdy/9sdy.dat

Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)