9NWD | pdb_00009nwd

Human E3 ligase UBR4-KCMF1-calmodulin complex (N-terminal)

• PDB DOI: https://doi.org/10.2210/pdb9NWD/pdb
• EM Map EMD-46688: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2025-03-22 Released: 2025-06-11 
• Deposition Author(s): Yang, Z., Haakonsen, D.L., Heider, M., Witus, S.R., Zelter, A., Beschauner, T., MacCoss, M.J., Rape, M.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), The G. Harold and Leila Y. Mathers Foundation

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Experimental Data Snapshot

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

Literature

Molecular basis of SIFI activity in the integrated stress response.

Yang, Z., Haakonsen, D.L., Heider, M., Witus, S.R., Zelter, A., Beschauner, T., MacCoss, M.J., Rape, M.

(2025) Nature 643: 1117-1126

• PubMed: 40328314 
• DOI: https://doi.org/10.1038/s41586-025-09074-z
• Primary Citation of Related Structures:  
  9D9Z, 9NWD, 9NWE


• PubMed Abstract: 
  

  Chronic stress response activation impairs cell survival and causes devastating degenerative diseases ^1-3 . Organisms accordingly deploy silencing factors, such as the E3 ubiquitin ligase silencing factor of the integrated stress response (SIFI), to terminate stress response signalling and ensure cellular homeostasis ⁴ . How a silencing factor can sense stress across cellular scales to elicit timely stress response inactivation is poorly understood. Here we combine cryo-electron microscopy analysis of endogenous SIFI with AlphaFold modelling and biochemical studies to report the structural and mechanistic basis of the silencing of the integrated stress response. SIFI detects both stress indicators and stress response components through flexible domains within an easily accessible scaffold, before building linkage-specific ubiquitin chains at separate, sterically restricted elongation modules. Ubiquitin handover by a ubiquitin-like domain couples versatile substrate modification to linkage-specific ubiquitin polymer formation. Stress response silencing therefore exploits a catalytic mechanism that is geared towards processing many diverse proteins and therefore allows a single enzyme to monitor and, if needed, modulate a complex cellular state.

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Organizational Affiliation: 
• Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.
Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
Biochemie-Zentrum der Universität Heidelberg (BZH), Heidelberg, Germany.
Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA. [e-mail].
Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA. [e-mail].
California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,148.92 kDa 
• Atom Count: 21,667 
• Modeled Residue Count: 2,783 
• Deposited Residue Count: 10,366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UBR4	A, B	5,183	Homo sapiens	Mutation(s): 0  EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T4S7 (Homo sapiens) Explore Q5T4S7  Go to UniProtKB:  Q5T4S7
PHAROS:  Q5T4S7 GTEx:  ENSG00000127481

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Yang, Z., Haakonsen, D.L., Heider, M., Witus, S.R., Zelter, A., Beschauner, T., MacCoss, M.J., Rape, M.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
The G. Harold and Leila Y. Mathers Foundation	United States	--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release
  
• Version 1.1: 2025-08-06
  Changes: Database references