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Structure paper

TitleIdentification of a cryptic allosteric site on the E3 ligase adapter protein cereblon
Journal, issue, pagesNature, Year 2025
Publish dateMay 22, 2025 (structure data deposition date)
AuthorsRizvi Z / Dippon VN / Choudhry AE / Chung CW / Alkuraya AF / Xu W / Tao XB / Jurewicz AJ / Schneck JL / Chen W ...Rizvi Z / Dippon VN / Choudhry AE / Chung CW / Alkuraya AF / Xu W / Tao XB / Jurewicz AJ / Schneck JL / Chen W / Curnutt NM / Kabir F / Chan KH / Queisser MA / Musetti C / Dai H / Benowitz AB / Woo CM / Lander GC
External linksNature / Search PubMed
MethodsEM (single particle)
Resolution2.21 - 3.39 Å
Structure data

EMDB-70776: DDB1-CRBN open NU refine map
Method: EM (single particle) / Resolution: 2.52 Å

EMDB-70777: DDB1-CRBN open local refinement
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-70778: DDB1-CRBNopen with lenalidomide
Method: EM (single particle) / Resolution: 2.52 Å

EMDB-70781: DDB1-CRBN intermediate NU
Method: EM (single particle) / Resolution: 2.71 Å

EMDB-70782: DDB1-CRBN[Closed] with lenalidomide and SB-405483- consensus refinement
Method: EM (single particle) / Resolution: 2.59 Å

EMDB-70783: DDB1-CRBN[Closed] with lenalidomide and SB-405483- Focused refine map
Method: EM (single particle) / Resolution: 2.21 Å

EMDB-70784: Composite map of DDB1-CRBN[Closed] in the presence of Lenalidomide and SB-405483
Method: EM (single particle) / Resolution: 2.59 Å

EMDB-70788: DDB1-CRBN-CK1a with lenalidomide and SB-405483
Method: EM (single particle) / Resolution: 2.92 Å

EMDB-70789: DDB1-CRBN-CK1a with lenalidomide and SB-405483 (Focused map)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-70790: DDB1-CRBN with casein kinase 1 alpha, lenalidomide, and SB-405483: composite map submission
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-70795: DDB1-CRBN with Ikaros ZF2-3, lenalidomide, and SB-405483: Consensus map
Method: EM (single particle) / Resolution: 2.97 Å

EMDB-70796: DDB1-CRBN with Ikaros(ZF2-3), lenalidomide, and SB-405483: focused map submission
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-70799: DDB1-CRBN with Ikaros ZF2-3, lenalidomide, and SB-405483; composite map submission
Method: EM (single particle) / Resolution: 2.97 Å

EMDB-70801: DDB1-CRBN with CK1a and DEG47
Method: EM (single particle) / Resolution: 2.78 Å

EMDB-70802: DDB1-CRBN with CK1a and DEG-47: focused map on CRBN
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-70803: DDB1-CRBN with CK1A and DEG-47: Focused map on CK1a
Method: EM (single particle) / Resolution: 3.39 Å

EMDB-70804: DDB1-CRBN with CK1a and DEG47: Composite map submission
Method: EM (single particle) / Resolution: 2.78 Å

EMDB-70827: DDB1-CRBN with CK1a, SB-405483, and DEG-47- consensus map submission
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-70835: DDB1-CRBN with CK1a, SB-405483, and DEG-47: focused map on CRBN
Method: EM (single particle) / Resolution: 3.03 Å

EMDB-70836: DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: Focused map on CK1 alpha
Method: EM (single particle) / Resolution: 3.08 Å

70862

9oty

EMDB-70862, PDB-9oty:
DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-70865: DDB1-CRBN with ikaros(ZF2) and DEG47- consensus map submission
Method: EM (single particle) / Resolution: 2.69 Å

EMDB-70866: DDB1-CRBN with Ikaros(ZF2) and DEG-47: focused map submission
Method: EM (single particle) / Resolution: 2.96 Å

70867

9ouk

EMDB-70867, PDB-9ouk:
DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission
Method: EM (single particle) / Resolution: 2.69 Å

EMDB-70868: DDB1-CRBN with ikaros, SB-405483, and DEG-47: consensus map submission
Method: EM (single particle) / Resolution: 2.97 Å

EMDB-70869: DDB1-CRBN with ikaros(ZF2) with SB-405483, and DEG-47: Focused map submission
Method: EM (single particle) / Resolution: 3.17 Å

70870

9oul

EMDB-70870, PDB-9oul:
DDB1-CRBN with Ikaros(ZF2), SB-405483, and DEG-47: composite map and model submission
Method: EM (single particle) / Resolution: 2.97 Å

Chemicals

ChemComp-ZN:
Unknown entry

PDB-1ceh:
STRUCTURE AND FUNCTION OF THE CATALYTIC SITE MUTANT ASP99ASN OF PHOSPHOLIPASE A2: ABSENCE OF CONSERVED STRUCTURAL WATER

PDB-1ceg:
CEPHALOTHIN COMPLEXED WITH DD-PEPTIDASE

PDB-1cek:
THREE-DIMENSIONAL STRUCTURE OF THE MEMBRANE-EMBEDDED M2 CHANNEL-LINING SEGMENT FROM THE NICOTINIC ACETYLCHOLINE RECEPTOR BY SOLID-STATE NMR SPECTROSCOPY

Source
  • homo sapiens (human)
KeywordsLIGASE / E3 ligases / Cullin RING Ligase / CRL4 / Cereblon / CRBN / molecular glues / IMiDs / Ikaros

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