当前蛋白身份：Q13422
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差异标签只比较当前检索结果；所有PDB和assembly原始记录仍分别保留。
相关结构差异明细
一行代表一个 PDB 条目中的一个 biological assembly；同一蛋白的多个单体会分别列出。
| PDB 条目 | Assembly / 聚集状态 | 构建体 | 突变与修饰 | 配体、离子与非聚合物 | 实验方法 | 实验环境 | 结构质量 |
|---|---|---|---|---|---|---|---|
| 6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) 提交 2018-07-09 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 C
97–130（34 aa）
|
未记录 | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION；293 K；Protein solution:
350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP
Crystallisation solution:
(Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
|
分辨率 3.25 Å R-free 0.234 |
| 6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) 提交 2018-07-09 | Assembly 2 蛋白异源复合物 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 F
97–130（34 aa）
|
未记录 | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION；293 K；Protein solution:
350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP
Crystallisation solution:
(Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
|
分辨率 3.25 Å R-free 0.234 |
| 6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) 提交 2018-07-09 | Assembly 3 蛋白异源复合物 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 I
97–130（34 aa）
|
未记录 | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION；293 K；Protein solution:
350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP
Crystallisation solution:
(Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
|
分辨率 3.25 Å R-free 0.234 |
| 6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) 提交 2018-07-09 | Assembly 4 蛋白异源复合物 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 L
97–130（34 aa）
|
未记录 | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION；293 K；Protein solution:
350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP
Crystallisation solution:
(Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
|
分辨率 3.25 Å R-free 0.234 |
| 8D7Z Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3 提交 2022-06-07 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 C
112–196（85 aa）
|
未记录 | ZN ZINC ION × 2 QFC Mezigdomide × 1 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM玻璃化条件
冷冻剂 ETHANE；Manual plunge in 4 degree C cold room
|
分辨率 3.10 Å |
| 8D80 Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3 提交 2022-06-07 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 C
112–196（85 aa）
|
未记录 | ZN ZINC ION × 2 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM玻璃化条件
冷冻剂 ETHANE；Manual plunge in 4 degree C cold room
|
分辨率 3.60 Å |
| 8RQC Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2 提交 2024-01-17 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 4 PDB 声明：tetrameric（4） 与蛋白数一致 |
链 B
141–174（34 aa）
链 E
141–174（34 aa）
|
未记录 | ZN ZINC ION × 4 QFC Mezigdomide × 2 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium sulphate, 25% (w/v) PEG 3350, and 0.1 M HEPES pH 7.5
|
分辨率 2.15 Å R-free 0.286 |
| 8TNP Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40 提交 2023-08-02 | Assembly 1 信息不足 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 C
143–178（36 aa）
|
突变：engineered to enhance binding of cereblon/DDB1 in the presence of IMiD derivatives | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM玻璃化条件
冷冻剂 ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
|
分辨率 3.30 Å |
| 8TNQ Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1 提交 2023-08-02 | Assembly 1 信息不足 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 C
143–178（36 aa）
|
突变：engineered to enhance binding of cereblon/DDB1 in the presence of IMiD derivatives | ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM玻璃化条件
冷冻剂 ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
|
分辨率 2.41 Å |
| 8TNR Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2 提交 2023-08-02 | Assembly 1 信息不足 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 C
143–178（36 aa）
|
突变：engineered to enhance binding of cereblon/DDB1 in the presence of IMiD derivatives | ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM玻璃化条件
冷冻剂 ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
|
分辨率 2.50 Å |
| 9OUK DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission 提交 2025-05-28 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 C
140–196（57 aa）
|
未记录 | ZN ZINC ION × 2 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM玻璃化条件
冷冻剂 ETHANE
|
分辨率 2.69 Å |
| 9Q2D Cryo-EM structure of ternary complex Ikaros-ZF2:CC-885:CRBN:DDB1 (molecular glue degrader) 提交 2025-08-15 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 A
112–196（85 aa）
|
未记录 | ZN ZINC ION × 2 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7
cryo-EM玻璃化条件
冷冻剂 ETHANE；blot time 4 sec
blot force 4
|
分辨率 2.94 Å |
| 9Y7D Cereblon with Golcadomide and Ikaros ZF1-2-3 提交 2025-09-09 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 C
83–196（114 aa）
|
未记录 | ZN ZINC ION × 2 A1AF4 Golcadomide × 1 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7
cryo-EM玻璃化条件
冷冻剂 NITROGEN
|
分辨率 3.26 Å |