← Back to search
9v0a

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

Method: ELECTRON MICROSCOPY
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

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 8 Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） Ubiquitin × 1 （P62979） DNA damage-binding protein 1 × 1 （Q16531） Cullin-4A × 1 （Q13619） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） ZINC ION × 6 S-Pomalidomide × 1 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 —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 26–427； UniProt 41–442

Ubiquitin-conjugating enzyme E2 D1

Homo sapiens

UniProt P51668

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Protein cereblon × 1 （Q96SW2） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） Ubiquitin × 1 （P62979） DNA damage-binding protein 1 × 1 （Q16531） Cullin-4A × 1 （Q13619） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） ZINC ION × 6 S-Pomalidomide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2c4p 2c4p

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2yho 2yho 2yho 2yho 3oj4 3oj4 3ptf 3ptf 4ap4 4qpl 4qpl 5fer

20 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UB2D1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–146； UniProt 2–147

Zinc finger protein Aiolos

Homo sapiens

UniProt Q9UKT9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） NEDD8 × 1 （Q15843） Ubiquitin × 1 （P62979） DNA damage-binding protein 1 × 1 （Q16531） Cullin-4A × 1 （Q13619） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） ZINC ION × 6 S-Pomalidomide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
9uum 9v0a 9v0b 9v0f

4 assemblies

View Construct and Data Evidence
UniProt name IKZF3_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain I； PDBConstruct 3–58； UniProt 142–197

NEDD8

Homo sapiens

UniProt Q15843

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） Ubiquitin × 1 （P62979） DNA damage-binding protein 1 × 1 （Q16531） Cullin-4A × 1 （Q13619） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） ZINC ION × 6 S-Pomalidomide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1ndd 1ndd 1ndd 1ndd 2ko3

5 assemblies

Homodimer

None

Homotetramer
1ndd

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1r4m 1r4m 1r4m 1r4m 1r4n 1r4n 1r4n 1r4n 1xt9 2bkr 2n7k 2nvu

66 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NEDD8_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain N； PDBConstruct 1–76； UniProt 1–76

Ubiquitin

Homo sapiens

UniProt P62979

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） DNA damage-binding protein 1 × 1 （Q16531） Cullin-4A × 1 （Q13619） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） ZINC ION × 6 S-Pomalidomide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3axc 7ooj 7ooj

3 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
22tu 28ln 28zu 28zv 28zx 28zy 3phw 3phw 3phw 3phw 3tbl 4r62

233 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RS27A_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain U； PDBConstruct 1–76； UniProt 1–76

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 8 Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） Ubiquitin × 1 （P62979） Cullin-4A × 1 （Q13619） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） ZINC ION × 6 S-Pomalidomide × 1 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 6
Chains and sequence ranges Author chain B； PDBConstruct 1–1140； UniProt 1–1140

Cullin-4A

Homo sapiens

UniProt Q13619

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） Ubiquitin × 1 （P62979） DNA damage-binding protein 1 × 1 （Q16531） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） ZINC ION × 6 S-Pomalidomide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2hye 4a0k 7okq 7opc 7opd 8b3g 8b3i 9eg8 9lwi 9lwj 9lwl 9pvh

16 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CUL4A_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain A； PDBConstruct 18–775； UniProt 2–759

E3 ubiquitin-protein ligase RBX1, N-terminally processed

Homo sapiens

UniProt P62877

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） Ubiquitin × 1 （P62979） DNA damage-binding protein 1 × 1 （Q16531） Cullin-4A × 1 （Q13619） ZINC ION × 6 S-Pomalidomide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2lgv

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ldj 1ldk 1ldk 1u6g 29hg 29hh 29hi 2hye 3dpl 3dqv 3dqv 3dqv

107 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RBX1_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain R； PDBConstruct 5–111； UniProt 2–108

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9v0a
Deposition date deposition_date2025-05-17
Structure title titleCryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly
Keywords keywordsMolecular glue degrader, pomalidomide, CRL4 ubiquitin ligase, DDB1, CRBN, Complex, LIGASE; LIGASE
Experimental Method methodELECTRON MICROSCOPY
▼

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.

9v0a__assembly_1__model_1

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

Download this curve (.dat)

9v0a__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

9v0a__assembly_1__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）54.53 Å
Rg (electron density)54.44 Å
Total Rg54.55 Å
Atom count20799
Residues2615
Excluded volume371790 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9v0a__assembly_1__model_1 octameric （8） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (10)

▶

7. Citations (1)