SAXSdb — 9sdx

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1. Structure Basics

entry_id	9sdx
deposition_date	2025-08-15
title	Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub
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	46.29 Å
rg_electron	46.34 Å
i0	345182000.00
molecular_weight	150710.0 kDa
excluded_volume	187900 Å³
envelope_volume	298060 Å³
shell_volume	55607 Å³
envelope_diameter	152.7 Å
shell_rg	48.21 Å
envelope_rg	45.38 Å
shape_rg	46.39 Å
total_rg	46.30 Å
total_atoms	10572
n_residues	1381
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	146.0 Å
rg_real	46.32 Å
rg_real_error	1.30 Å
i0_real	3.4520e+08
i0_real_error	6.6860e+06
rg_reciprocal	46.30 Å
i0_reciprocal	345200000.0000
total_estimate	0.6389
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	55.8 Å
skewness	0.219
kurtosis	-0.673
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	27760000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 0.002; Positv: 1.000; Valcen: 0.991; Smooth: 0.382

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	NEDD8
formula_weight	9086.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N
atom_count	10572

MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGGGGLRQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
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	Ubiquitin
formula_weight	8519.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	U

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	L3A2-1
formula_weight	17998.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

GSMVAASSRLMKELEEIRKAGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFAKNAEEFTKKYGEKRPVD

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 5 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 6 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 7 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	7

Entity 8 non-polymer

description	5-azanylpentan-2-one
formula_weight	101.1 kDa
src_method	syn
entity_count	1

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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	2.970 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.97 Å
resolution_method	—
num_particles	200442

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

Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub

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 (8)

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 polymer

Polymer

Source

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)