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9t7v

Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub

Method: ELECTRON MICROSCOPY D_max: 201.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t7v
deposition_date	2025-11-12
title	Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub
keywords	Cullin, E3 ligase, Ubiquitin, 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	58.06 Å
rg_electron	58.48 Å
i0	662957000.00
molecular_weight	214530.0 kDa
excluded_volume	268180 Å³
envelope_volume	473840 Å³
shell_volume	69396 Å³
envelope_diameter	199.0 Å
shell_rg	60.32 Å
envelope_rg	55.54 Å
shape_rg	58.54 Å
total_rg	58.33 Å
total_atoms	15047
n_residues	1893
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	201.8 Å
rg_real	58.23 Å
rg_real_error	2.85 Å
i0_real	6.6300e+08
i0_real_error	1.4020e+07
rg_reciprocal	57.89 Å
i0_reciprocal	662600000.0000
total_estimate	0.8585
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	74.8 Å
skewness	0.295
kurtosis	-0.437
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0000
highest_alpha	26530000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.929; Smooth: 0.610

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4. Crystallography & Experiment

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5. Entities & Polymer Info (12)

Entity 1 polymer

description	Cysteine dioxygenase type 1
formula_weight	22867.6 kDa
ec_number	1.13.11.20
mutation	K8C, C76A, C93S, C130A, C164S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	15047

MEQTEVLCPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTRNLVDQGNGKFNLMILAWGEGHGSSIHDHTNSHSFLKMLQGNLKETLFAWPDKKSNEMVKKSERVLRENQAAYINDSVGLHRVENISHTEPAVSLHLYSPPFDTSHAFDQRTGHKNKVTMTFHSKFGIRTPNATSGSLENN

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	12280.9 kDa
ec_number	2.3.2.27,2.3.2.32
mutation	N-terminal residues 1-4 deleted
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

EDGEETCALASHSGSSGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK

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	Elongin-C
formula_weight	12485.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	O

MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 5 polymer

description	NEDD8
formula_weight	8574.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 6 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 7 polymer

description	E3 ubiquitin-protein ligase ARIH2
formula_weight	57735.7 kDa
ec_number	2.3.2.31
mutation	L381A,E382A,E455A,
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MSVDMNSQGSDSNEEDYDPNCEEEEEEEEDDPGDIEDYYVGVASDVEQQGADAFDPEEYQFTCLTYKESEGALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEARVQPNPSKHVPTSHPPHHCAVCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVGVSCMAQDCPLRTPEDFVFPLLPNEELREKYRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQAREALKKYLFYFERWENHNKSLQAAAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAKCRYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIANLSWKVERADSYDRGDLENQMHIAEQRRRTLLKDFHDT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 8 polymer

description	Elongin-B
formula_weight	13147.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 9 polymer

description	Leucine-rich repeat-containing protein 58
formula_weight	40626.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MEEAGAAVVTAGEAELNWSRLSVSTETLESELEARGEERRGAREALLRLLLPHNRLVSLPRALGSGFPHLQLLDVSGNALTALGPELLALRGLRTLLAKNNRLGGPSALPKGLAQSPLCRSLQVLNLSGNCFQEVPASLLELRALQTLSLGGNQLQSIPAEIENLQSLECLYLGGNFIKEIPPELGNLPSLNYLVLCDNKIQSIPPQLSQLHSLRSLSLHNNLLTYLPREILNLIHLEELSLRGNPLVVRFVRDLTYDPPTLLELAARTIKIRNISYTPYDLPGNLLRYLGSASNCPNPKCGGVYFDCCVRQIKFVDFCGKYRLPLMHYLCSPECSSPCSSASHSSTSQSESDSEDEASVAARRMQKVLLG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 10 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 11 non-polymer

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

Entity 12 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	8

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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	triclinic

resolution	2.95 Å
resolution_method	—
num_particles	847022

fit	/app/data/saxs_computation/t7/9t7v/9t7v.fit
pddf	/app/data/pr_computation/t7/9t7v/9t7v.pr.out
profile	/app/data/saxs_computation/t7/9t7v/9t7v.dat

Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-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

EM 3D

5. Entities & Polymer Info (12)

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 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

Entity 9 polymer

Polymer

Source

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)