9H59 | pdb_00009h59

Cryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7

• PDB DOI: https://doi.org/10.2210/pdb9H59/pdb
• EM Map EMD-51881: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-22 Released: 2025-06-25 
• Deposition Author(s): Khoshouei, M., Schroeder, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A cereblon (CRBN) molecular glue degrader of NIMA-related kinase 7 (NEK7) reveals a context-dependent role in NLRP3 inflammasome activation

Sylvain, A., Stoehr, N., Ma, F., Cernijenko, A., Schroder, M., Khoshouei, M., Vogelsanger, M., Schoenboerner, M., Burke, A., Pasupuleti, R., Solomon, J., Paulk, J., Xu, L., Dawson, J., Begue, D., Lefeuvre, P., Ahrne, E., Hofmann, A., Dickson, C.J., Arabin, P., Zimmerlin, A., Kiffe, M., Froehlicher, M., Boersig, T., Elhajouji, A., Brichet, M., Menon, S., Liu, S., Mueller, M., Wartchow, C., Lin, J., Cardona Gloria, Y., Dickhofer, S., Weber, A.N.R., Welzel, T., Kuemmerle-Deschner, J., Farady, C.J., Pulz, R., Bornancin, F., Buckley, D.L., Bassi, Z.I.

(2024) bioRxiv 

• DOI: https://doi.org/10.1101/2024.11.06.622079

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 214.78 kDa 
• Atom Count: 13,425 
• Modeled Residue Count: 1,793 
• Deposited Residue Count: 1,903 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A	1,140	Homo sapiens	Mutation(s): 0  Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531  Go to UniProtKB:  Q16531
GTEx:  ENSG00000167986

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Nek7	B [auth C]	304	Homo sapiens	Mutation(s): 0  Gene Names: NEK7 EC: 2.7.11.34
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDX7 (Homo sapiens) Explore Q8TDX7  Go to UniProtKB:  Q8TDX7
GTEx:  ENSG00000151414

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	C [auth B]	459	Homo sapiens	Mutation(s): 0  Gene Names: CRBN, AD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens) Explore Q96SW2  Go to UniProtKB:  Q96SW2
GTEx:  ENSG00000113851

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ISP (Subject of Investigation/LOI)	D [auth B]	2-[(3S)-2,6-bis(oxidanylidene)piperidin-3-yl]-5-[(1S,2R,5S)-2-(ethylamino)-8-azabicyclo[3.2.1]octan-8-yl]isoindole-1,3-dione C22 H26 N4 O4 QAKJEKTXKXAPBP-LSZYVWPRSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Khoshouei, M., Schroeder, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release
  
• Version 1.1: 2025-07-09
  Changes: Data collection
• Version 1.2: 2026-08-05
  Changes: Data collection, Database references