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

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

Khoshouei, M., Schroeder, M.

To be published.

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
PHAROS:  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
PHAROS:  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
PHAROS:  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