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9e2u

Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3)

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA damage-binding protein 1

Homo sapiens

UniProt Q16531

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 4 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 3 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 3 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 4 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3e0c 8zsw 9bbe 9bbg 9bbh 9bbi 9ejq 9zxm 9zxn

9 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
10ay 2hye 3ei1 3ei2 3ei3 3ei4 3ei4 3ei4 3i7h 3i7k 3i7l 3i7n

282 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DDB1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 29–423； UniProt 1–395 Author chain A； PDBConstruct 430–864； UniProt 706–1140 Author chain C； PDBConstruct 29–423； UniProt 1–395 Author chain C； PDBConstruct 430–864； UniProt 706–1140 Author chain E； PDBConstruct 29–423； UniProt 1–395 Author chain E； PDBConstruct 430–864； UniProt 706–1140 Author chain G； PDBConstruct 29–423； UniProt 1–395 Author chain G； PDBConstruct 430–864； UniProt 706–1140 Author chain I； PDBConstruct 29–423； UniProt 1–395 Author chain I； PDBConstruct 430–864； UniProt 706–1140 Author chain K； PDBConstruct 29–423； UniProt 1–395 Author chain K； PDBConstruct 430–864； UniProt 706–1140 Author chain M； PDBConstruct 29–423； UniProt 1–395 Author chain M； PDBConstruct 430–864； UniProt 706–1140 Author chain O； PDBConstruct 29–423； UniProt 1–395 Author chain O； PDBConstruct 430–864； UniProt 706–1140

Protein cereblon

Homo sapiens

UniProt Q96SW2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 4 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 3 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 3 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 4 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Zinc finger protein Helios × 1 ;3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide ; × 1 ZINC ION × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
8rq1 8rq8 8rqa 9gy3 9gy3 9odr 9odr 9odr 9odr 9ods 9ods 9ods

14 assemblies; showing the first 12

Homodimer
9gao

1 assemblies

Homotetramer

None

Other homooligomers
9cuo 9cuo

2 assemblies

Heteromeric or nucleic-acid complex
10ay 11mr 4m91 4tz4 5fqd 5fqd 5hxb 5hxb 5v3o 6bn7 6bn8 6bn9

125 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CRBN_HUMAN
Isoform Q96SW2-2
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 23–463； UniProt 1–441 Author chain D； PDBConstruct 23–463； UniProt 1–441 Author chain F； PDBConstruct 23–463； UniProt 1–441 Author chain H； PDBConstruct 23–463； UniProt 1–441 Author chain J； PDBConstruct 23–463； UniProt 1–441 Author chain L； PDBConstruct 23–463； UniProt 1–441 Author chain N； PDBConstruct 23–463； UniProt 1–441 Author chain P； PDBConstruct 23–463； UniProt 1–441

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_id9e2u
Deposition date deposition_date2024-10-23
Last revision last_revision2025-09-03
Structure title titleCrystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3)
Keywords keywordsCRBN, DDB1, IKZF2, ALV1, DEGRADATION, E3 LIGASE, LIGASE, MOLECULAR GLUE; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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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.

9e2u__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9e2u__assembly_4__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

9e2u__assembly_4__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）36.92 Å
Rg (electron density)36.22 Å
Total Rg36.87 Å
Atom count10305
Residues1300
Excluded volume183430 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9e2u__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 9e2u__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 9e2u__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 9e2u__assembly_4__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 9e2u__assembly_5__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 9e2u__assembly_6__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 9e2u__assembly_7__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 9e2u__assembly_8__model_1 trimeric （3） 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 (5)

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7. Citations (2)