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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9H59

This is version 1.1 of the entry. See complete history.

Literature

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

Khoshouei, M., Schroeder, M.

To be published.

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16531
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TDX7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96SW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ISP (Subject of Investigation/LOI) Query on A1ISP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	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		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-06-25
Type: Initial release
Version 1.1: 2025-07-09
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.