9t7v

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

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cysteine dioxygenase type 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	RING-box protein 2 × 1 （Q9UBF6） Ubiquitin × 1 （P0CG48） Elongin-C × 1 （Q15369） NEDD8 × 1 （Q15843） Cullin-5 × 1 （Q93034） E3 ubiquitin-protein ligase ARIH2 × 1 （O95376） Elongin-B × 1 （Q15370） Leucine-rich repeat-containing protein 58 × 1 （Q96CX6） FE (III) ION × 1 5-azanylpentan-2-one × 1 ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDO1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–200； UniProt 1–200

RING-box protein 2

Homo sapiens

UniProt Q9UBF6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Cysteine dioxygenase type 1 × 1 （Q16878） Ubiquitin × 1 （P0CG48） Elongin-C × 1 （Q15369） NEDD8 × 1 （Q15843） Cullin-5 × 1 （Q93034） E3 ubiquitin-protein ligase ARIH2 × 1 （O95376） Elongin-B × 1 （Q15370） Leucine-rich repeat-containing protein 58 × 1 （Q96CX6） FE (III) ION × 1 5-azanylpentan-2-one × 1 ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBX2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain R； PDBConstruct 1–109； UniProt 5–113

Ubiquitin

Homo sapiens

UniProt P0CG48

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Cysteine dioxygenase type 1 × 1 （Q16878） RING-box protein 2 × 1 （Q9UBF6） Elongin-C × 1 （Q15369） NEDD8 × 1 （Q15843） Cullin-5 × 1 （Q93034） E3 ubiquitin-protein ligase ARIH2 × 1 （O95376） Elongin-B × 1 （Q15370） Leucine-rich repeat-containing protein 58 × 1 （Q96CX6） FE (III) ION × 1 5-azanylpentan-2-one × 1 ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain U； PDBConstruct 1–75； UniProt 1–75

Elongin-C

Homo sapiens

UniProt Q15369

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Cysteine dioxygenase type 1 × 1 （Q16878） RING-box protein 2 × 1 （Q9UBF6） Ubiquitin × 1 （P0CG48） NEDD8 × 1 （Q15843） Cullin-5 × 1 （Q93034） E3 ubiquitin-protein ligase ARIH2 × 1 （O95376） Elongin-B × 1 （Q15370） Leucine-rich repeat-containing protein 58 × 1 （Q96CX6） FE (III) ION × 1 5-azanylpentan-2-one × 1 ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOC_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain O； PDBConstruct 1–112； UniProt 1–112

NEDD8

Homo sapiens

UniProt Q15843

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Cysteine dioxygenase type 1 × 1 （Q16878） RING-box protein 2 × 1 （Q9UBF6） Ubiquitin × 1 （P0CG48） Elongin-C × 1 （Q15369） Cullin-5 × 1 （Q93034） E3 ubiquitin-protein ligase ARIH2 × 1 （O95376） Elongin-B × 1 （Q15370） Leucine-rich repeat-containing protein 58 × 1 （Q96CX6） FE (III) ION × 1 5-azanylpentan-2-one × 1 ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEDD8_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain N； PDBConstruct 1–76； UniProt 1–76

Cullin-5

Homo sapiens

UniProt Q93034

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Cysteine dioxygenase type 1 × 1 （Q16878） RING-box protein 2 × 1 （Q9UBF6） Ubiquitin × 1 （P0CG48） Elongin-C × 1 （Q15369） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase ARIH2 × 1 （O95376） Elongin-B × 1 （Q15370） Leucine-rich repeat-containing protein 58 × 1 （Q96CX6） FE (III) ION × 1 5-azanylpentan-2-one × 1 ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CUL5_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain C； PDBConstruct 1–780； UniProt 1–780

E3 ubiquitin-protein ligase ARIH2

Homo sapiens

UniProt O95376

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Cysteine dioxygenase type 1 × 1 （Q16878） RING-box protein 2 × 1 （Q9UBF6） Ubiquitin × 1 （P0CG48） Elongin-C × 1 （Q15369） NEDD8 × 1 （Q15843） Cullin-5 × 1 （Q93034） Elongin-B × 1 （Q15370） Leucine-rich repeat-containing protein 58 × 1 （Q96CX6） FE (III) ION × 1 5-azanylpentan-2-one × 1 ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARI2_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain H； PDBConstruct 1–493； UniProt 1–493

Elongin-B

Homo sapiens

UniProt Q15370

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Cysteine dioxygenase type 1 × 1 （Q16878） RING-box protein 2 × 1 （Q9UBF6） Ubiquitin × 1 （P0CG48） Elongin-C × 1 （Q15369） NEDD8 × 1 （Q15843） Cullin-5 × 1 （Q93034） E3 ubiquitin-protein ligase ARIH2 × 1 （O95376） Leucine-rich repeat-containing protein 58 × 1 （Q96CX6） FE (III) ION × 1 5-azanylpentan-2-one × 1 ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOB_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain I； PDBConstruct 1–118； UniProt 1–118

Leucine-rich repeat-containing protein 58

Homo sapiens

UniProt Q96CX6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Cysteine dioxygenase type 1 × 1 （Q16878） RING-box protein 2 × 1 （Q9UBF6） Ubiquitin × 1 （P0CG48） Elongin-C × 1 （Q15369） NEDD8 × 1 （Q15843） Cullin-5 × 1 （Q93034） E3 ubiquitin-protein ligase ARIH2 × 1 （O95376） Elongin-B × 1 （Q15370） FE (III) ION × 1 5-azanylpentan-2-one × 1 ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LRC58_HUMAN
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain B； PDBConstruct 1–371； UniProt 1–371

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9t7v
Deposition date deposition_date	2025-11-12
Structure title title	Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub
Keywords keywords	Cullin, E3 ligase, Ubiquitin, LIGASE; LIGASE
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9t7v__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9t7v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9t7v__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	58.06 Å
Rg (electron density)	58.48 Å
Total Rg	58.33 Å
Atom count	15047
Residues	1893
Excluded volume	268180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9t7v__assembly_1__model_1`	nonameric （9）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	Cysteine dioxygenase type 1
Molecular weight formula_weight	22867.6 kDa
EC 编号 ec_number	1.13.11.20
Mutation mutation	K8C, C76A, C93S, C130A, C164S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	15047

MEQTEVLCPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTRNLVDQGNGKFNLMILAWGEGHGSSIHDHTNSHSFLKMLQGNLKETLFAWPDKKSNEMVKKSERVLRENQAAYINDSVGLHRVENISHTEPAVSLHLYSPPFDTSHAFDQRTGHKNKVTMTFHSKFGIRTPNATSGSLENN

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RING-box protein 2
Molecular weight formula_weight	12280.9 kDa
EC 编号 ec_number	2.3.2.27,2.3.2.32
Mutation mutation	N-terminal residues 1-4 deleted
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

EDGEETCALASHSGSSGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8519.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Elongin-C
Molecular weight formula_weight	12485.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 5 Entity 5 polymer

Description description	NEDD8
Molecular weight formula_weight	8574.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Cullin-5
Molecular weight formula_weight	91085.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MATSNLLKNKGSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAKIHQALKEDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMGKQGSNKKSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGVRESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKEEEKRALRYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNGIEPMLKDLEEHIISAGLADMVAAAETITTDSEKYVEQLLTLFNRFSKLVKEAFQDDPRFLTARDKAYKAVVNDATIFKLELPLKQKGVGLKTQPESKCPELLANYCDMLLRKTPLSKKLTSEEIEAKLKEVLLVLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWSRSSEKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 7 Entity 7 polymer

Description description	E3 ubiquitin-protein ligase ARIH2
Molecular weight formula_weight	57735.7 kDa
EC 编号 ec_number	2.3.2.31
Mutation mutation	L381A,E382A,E455A,
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSVDMNSQGSDSNEEDYDPNCEEEEEEEEDDPGDIEDYYVGVASDVEQQGADAFDPEEYQFTCLTYKESEGALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEARVQPNPSKHVPTSHPPHHCAVCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVGVSCMAQDCPLRTPEDFVFPLLPNEELREKYRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQAREALKKYLFYFERWENHNKSLQAAAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAKCRYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIANLSWKVERADSYDRGDLENQMHIAEQRRRTLLKDFHDT

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Elongin-B
Molecular weight formula_weight	13147.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 9 Entity 9 polymer

Description description	Leucine-rich repeat-containing protein 58
Molecular weight formula_weight	40626.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEEAGAAVVTAGEAELNWSRLSVSTETLESELEARGEERRGAREALLRLLLPHNRLVSLPRALGSGFPHLQLLDVSGNALTALGPELLALRGLRTLLAKNNRLGGPSALPKGLAQSPLCRSLQVLNLSGNCFQEVPASLLELRALQTLSLGGNQLQSIPAEIENLQSLECLYLGGNFIKEIPPELGNLPSLNYLVLCDNKIQSIPPQLSQLHSLRSLSLHNNLLTYLPREILNLIHLEELSLRGNPLVVRFVRDLTYDPPTLLELAARTIKIRNISYTPYDLPGNLLRYLGSASNCPNPKCGGVYFDCCVRQIKFVDFCGKYRLPLMHYLCSPECSSPCSSASHSSTSQSESDSEDEASVAARRMQKVLLG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 10 Entity 10 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	5-azanylpentan-2-one
Molecular weight formula_weight	101.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.95 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	847022

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cysteine dioxygenase type 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RING-box protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NEDD8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cullin-5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

E3 ubiquitin-protein ligase ARIH2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Leucine-rich repeat-containing protein 58

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9t7v__assembly_1__model_1

9t7v__assembly_1__model_1 | I(q)

9t7v__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment