9UUM | pdb_00009uum

Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly

PDB DOI: https://doi.org/10.2210/pdb9UUM/pdb
EM Map EMD-64512: EMDB EMDataResource

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

Deposited: 2025-05-07 Released: 2026-06-10
Deposition Author(s): Deng, Z.H., Ai, H.S., Liu, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.41 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

Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly

Deng, Z.H., Ai, H.S., Liu, L.

To be published.

Macromolecule Content

Total Structure Weight: 318.95 kDa
Atom Count: 20,807
Modeled Residue Count: 2,620
Deposited Residue Count: 2,809
Unique protein chains: 8

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A [auth C]	427	Homo sapiens	Mutation(s): 0 Gene Names: CRBN, AD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens) Explore Q96SW2 Go to UniProtKB: Q96SW2
PHAROS: Q96SW2 GTEx: ENSG00000113851
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96SW2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D1	B [auth D]	146	Homo sapiens	Mutation(s): 0 Gene Names: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P51668 (Homo sapiens) Explore P51668 Go to UniProtKB: P51668
PHAROS: P51668 GTEx: ENSG00000072401
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51668
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein Aiolos	C [auth I]	58	Homo sapiens	Mutation(s): 0 Gene Names: IKZF3, ZNFN1A3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKT9 (Homo sapiens) Explore Q9UKT9 Go to UniProtKB: Q9UKT9
PHAROS: Q9UKT9 GTEx: ENSG00000161405
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UKT9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD8	D [auth N]	76	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15843
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	E [auth U]	76	Homo sapiens	Mutation(s): 0 Gene Names: RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens) Explore P62979 Go to UniProtKB: P62979
PHAROS: P62979 GTEx: ENSG00000143947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62979
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBX1, N-terminally processed	F [auth R]	111	Homo sapiens	Mutation(s): 0 Gene Names: RBX1, RNF75, ROC1 EC: 2.3.2.32 (UniProt), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P62877 (Homo sapiens) Explore P62877 Go to UniProtKB: P62877
PHAROS: P62877 GTEx: ENSG00000100387
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62877
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	G [auth B]	1,140	Homo sapiens	Mutation(s): 0 Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531 Go to UniProtKB: Q16531
PHAROS: Q16531 GTEx: ENSG00000167986
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16531
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-4A	H [auth A]	775	Homo sapiens	Mutation(s): 0 Gene Names: CUL4A
UniProt & NIH Common Fund Data Resources
Find proteins for Q13619 (Homo sapiens) Explore Q13619 Go to UniProtKB: Q13619
PHAROS: Q13619 GTEx: ENSG00000139842
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13619
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QFC (Subject of Investigation/LOI) Query on QFC Download:Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	Mezigdomide C₃₂ H₃₀ F N₅ O₄ YTINZZFBHWSAGL-NDEPHWFRSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain K [auth I] SDF format, chain L [auth I] SDF format, chain M [auth R] SDF format, chain N [auth R] SDF format, chain O [auth R] MOL2 format, chain I [auth C] MOL2 format, chain K [auth I] MOL2 format, chain L [auth I] MOL2 format, chain M [auth R] MOL2 format, chain N [auth R] MOL2 format, chain O [auth R] mmCIF format, chain I [auth C] mmCIF format, chain K [auth I] mmCIF format, chain L [auth I] mmCIF format, chain M [auth R] mmCIF format, chain N [auth R] mmCIF format, chain O [auth R]	I [auth C] K [auth I] L [auth I] M [auth R] N [auth R] I [auth C], K [auth I], L [auth I], M [auth R], N [auth R], O [auth R]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain K [auth I] Focus chain L [auth I] Focus chain M [auth R] Focus chain N [auth R] Focus chain O [auth R] Interactions & Density Focus chain I [auth C] Focus chain K [auth I] Focus chain L [auth I] Focus chain M [auth R] Focus chain N [auth R] Focus chain O [auth R]