ISDA: 9V0E

Deposition Date 2025-05-17

Release Date 2026-08-19

Last Version Date 2026-08-19

Entry Detail

PDB ID:

9V0E

Keywords:

LIGASE

Title:

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

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli, Homo sapiens

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.51 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:Cullin-4A
Chain IDs:A
Chain Length:775
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:DNA damage-binding protein 1
Chain IDs:B
Chain Length:1140
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:Protein cereblon
Chain IDs:C
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-conjugating enzyme
Chain IDs:D
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:Zinc finger protein Aiolos
Chain IDs:E (auth: I)
Chain Length:58
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:NEDD8
Chain IDs:F (auth: N)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase R
Chain IDs:G (auth: R)
Chain Length:111
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Chain IDs:H (auth: U)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules

A1AF4

Primary Citation

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

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

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