9PTU | pdb_00009ptu

Cryo-EM structure of the DCAF11 E3 ligase bound to the DDX18 helicase mediated by GSH-M12

• PDB DOI: https://doi.org/10.2210/pdb9PTU/pdb
• EM Map EMD-71847: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2025-07-29 Released: 2026-07-01 
• Deposition Author(s): Wachter, F., Jin, C.Y., Yoon, H., Ebert, B.L., Fischer, E.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental

Literature

Cryo-EM structure of the DCAF11 E3 ligase bound to the DDX18 helicase mediated by GSH-M12

Wachter, F., Jin, C.Y., Yoon, H., Ebert, B.L., Fischer, E.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: 217.82 kDa 
• Atom Count: 11,462 
• Modeled Residue Count: 1,426 
• Deposited Residue Count: 1,932 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DDB1- and CUL4-associated factor 11	A	590	Homo sapiens	Mutation(s): 0  Gene Names: DCAF11, WDR23, GL014, PRO2389
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEB1 (Homo sapiens) Explore Q8TEB1  Go to UniProtKB:  Q8TEB1
PHAROS:  Q8TEB1 GTEx:  ENSG00000100897

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX18	B [auth C]	478	Homo sapiens	Mutation(s): 0  Gene Names: DDX18, cPERP-D EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVP1 (Homo sapiens) Explore Q9NVP1  Go to UniProtKB:  Q9NVP1
PHAROS:  Q9NVP1 GTEx:  ENSG00000088205

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	C [auth B]	864	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CK5( Subject of Investigation/LOI)	D [auth A]	L-gamma-glutamyl-S-{6-chloro-5-[(3,5-dimethylphenoxy)carbonyl]-3-fluoropyridin-2-yl}-L-cysteinylglycine C24 H26 Cl F N4 O8 S QIYLQVBXFUXWOQ-IRXDYDNUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419+SVN
RECONSTRUCTION	cryoSPARC	4.6.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-01 
Deposition Author(s): Wachter, F., Jin, C.Y., Yoon, H., Ebert, B.L., Fischer, E.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1 K99GM154065-01A1
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5R01CA214608-09

Revision History  

• Version 1.0: 2026-07-01
  Type: Initial release