9SDX | pdb_00009sdx

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

PDB DOI: https://doi.org/10.2210/pdb9SDX/pdb
EM Map EMD-54793: EMDB EMDataResource

Classification: LIGASE
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli, Trichoplusia ni
Mutation(s): No

Deposited: 2025-08-15 Released: 2025-12-24
Deposition Author(s): Schulman, B.A., Du, J.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.97 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

E2 Variants for Probing E3 Ubiquitin Ligase Activities

Du, J., Schulman, B.A.

To be published.

Macromolecule Content

Total Structure Weight: 197.84 kDa
Atom Count: 10,572
Modeled Residue Count: 1,381
Deposited Residue Count: 1,699
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD8	A [auth N]	81	Homo sapiens	Mutation(s): 0 Gene Names: NEDD8
UniProt & NIH Common Fund Data Resources
Find proteins for Q15843 (Homo sapiens) Explore Q15843 Go to UniProtKB: Q15843
PHAROS: Q15843 GTEx: ENSG00000129559
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15843
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RING-box protein 2	B [auth R]	113	Homo sapiens	Mutation(s): 0 Gene Names: RNF7, RBX2, ROC2, SAG EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBF6 (Homo sapiens) Explore Q9UBF6 Go to UniProtKB: Q9UBF6
PHAROS: Q9UBF6 GTEx: ENSG00000114125
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UBF6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C [auth U]	75	Homo sapiens	Mutation(s): 0 Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
PHAROS: P0CG48 GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG48
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
L3A2-1	D [auth G]	157	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-5	E [auth C]	780	Homo sapiens	Mutation(s): 0 Gene Names: CUL5, VACM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q93034 (Homo sapiens) Explore Q93034 Go to UniProtKB: Q93034
PHAROS: Q93034 GTEx: ENSG00000166266
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q93034
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase ARIH2	F [auth H]	493	Homo sapiens	Mutation(s): 0 Gene Names: ARIH2, ARI2, TRIAD1, HT005 EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for O95376 (Homo sapiens) Explore O95376 Go to UniProtKB: O95376
PHAROS: O95376 GTEx: ENSG00000177479
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95376
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SY8 (Subject of Investigation/LOI) Query on SY8 Download Ideal Coordinates CCD File SDF format, chain J [auth U] MOL2 format, chain J [auth U] mmCIF format, chain J [auth U]	J [auth U]	5-azanylpentan-2-one C₅ H₁₁ N O VTHKLCWOLNQWHB-UHFFFAOYSA-N		Interactions Focus chain J [auth U] Interactions & Density Focus chain J [auth U]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth R] SDF format, chain H [auth R] SDF format, chain I [auth R] SDF format, chain K [auth H] SDF format, chain M [auth H] SDF format, chain N [auth H] SDF format, chain L [auth H] MOL2 format, chain G [auth R] MOL2 format, chain H [auth R] MOL2 format, chain I [auth R] MOL2 format, chain K [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H] MOL2 format, chain L [auth H] mmCIF format, chain G [auth R] mmCIF format, chain H [auth R] mmCIF format, chain I [auth R] mmCIF format, chain K [auth H] mmCIF format, chain M [auth H] mmCIF format, chain N [auth H] mmCIF format, chain L [auth H]	G [auth R] H [auth R] I [auth R] K [auth H] L [auth H] G [auth R], H [auth R], I [auth R], K [auth H], L [auth H], M [auth H], N [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth R] Focus chain H [auth R] Focus chain I [auth R] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Interactions & Density Focus chain G [auth R] Focus chain H [auth R] Focus chain I [auth R] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H]