ISDA: 9V0A

Deposition Date 2025-05-17

Release Date 2026-06-10

Last Version Date 2026-06-10

Entry Detail

PDB ID:

9V0A

Keywords:

LIGASE

Title:

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

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

Homo sapiens, Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.69 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cullin-4A
Gene (Uniprot):CUL4A
Chain IDs:G (auth: A)
Chain Length:775
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13619 Pfam ID:PF00888, PF26557, PF10557

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA damage-binding protein 1
Gene (Uniprot):DDB1
Chain IDs:F (auth: B)
Chain Length:1140
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q16531 Pfam ID:PF10433, PF23726, PF03178

Structures with similar UniProt ID

Protein Blast

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

UniProt ID:Q96SW2 Pfam ID:PF02190, PF03226

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-conjugating enzyme
Gene (Uniprot):UBE2D1
Chain IDs:B (auth: D)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P51668 Pfam ID:PF00179 EC:2.3.2.23

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Zinc finger protein Aiolos
Gene (Uniprot):IKZF3
Chain IDs:C (auth: I)
Chain Length:58
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9UKT9 Pfam ID:PF00096

Structures with similar UniProt ID

Protein Blast

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

UniProt ID:Q15843 Pfam ID:PF00240

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase R
Gene (Uniprot):RBX1
Chain IDs:H (auth: R)
Chain Length:111
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62877 Pfam ID:PF12678 EC:2.3.2.27

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Gene (Uniprot):RPS27A
Chain IDs:E (auth: U)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62979 Pfam ID:PF00240

Ligand Molecules