9HJ0 | pdb_00009hj0

Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with Samuraciclib

• PDB DOI: https://doi.org/10.2210/pdb9HJ0/pdb
• EM Map EMD-52207: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2024-11-27 Released: 2025-08-20 
• Deposition Author(s): Cushing, V.I., Greber, B.J., Ali, S., Lai, C.-F., Bevan, C.L., Coombes, R.C., Buluwela, L.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Mutation of CDK7 at a conserved residue identifies a common mechanism of acquired resistance to CDK inhibitors in cancer

Lai, C.-F., Cushing, V.I., Bevan, C.L., Coombes, R.C., Greber, B.J., Buluwela, L., Ali, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 87.71 kDa 
• Atom Count: 5,070 
• Modeled Residue Count: 619 
• Deposited Residue Count: 766 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CDK-activating kinase assembly factor MAT1	A [auth H]	93	Homo sapiens	Mutation(s): 0  Gene Names: MNAT1, CAP35, MAT1, RNF66
UniProt & NIH Common Fund Data Resources
Find proteins for P51948 (Homo sapiens) Explore P51948  Go to UniProtKB:  P51948
PHAROS:  P51948 GTEx:  ENSG00000020426

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-H	B [auth I]	324	Homo sapiens	Mutation(s): 1  Gene Names: CCNH
UniProt & NIH Common Fund Data Resources
Find proteins for P51946 (Homo sapiens) Explore P51946  Go to UniProtKB:  P51946
PHAROS:  P51946 GTEx:  ENSG00000134480

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 7	C [auth J]	349	Homo sapiens	Mutation(s): 1  Gene Names: CDK7, CAK, CAK1, CDKN7, MO15, STK1 EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P50613 (Homo sapiens) Explore P50613  Go to UniProtKB:  P50613
PHAROS:  P50613 GTEx:  ENSG00000134058

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I74 (Subject of Investigation/LOI)	D [auth J]	(3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol C22 H30 N6 O YCVGLKWJKIKVBI-MJGOQNOKSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	RELION	5.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Cushing, V.I., Greber, B.J., Ali, S., Lai, C.-F., Bevan, C.L., Coombes, R.C., Buluwela, L.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/V009354/1

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release