9E5A | pdb_00009e5a

Crystal structure of Acanthamoeba polyphaga mimivirus (APMV) vIF4G 53-312

• PDB DOI: https://doi.org/10.2210/pdb9E5A/pdb

• Classification: TRANSLATION
• Organism(s): Acanthamoeba polyphaga mimivirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-28 Released: 2026-02-25 
• Deposition Author(s): Fels, J.M., Hill, A.B., Kranzusch, P.J., Lee, A.S.Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: in silico

Literature

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life.

Fels, J.M., Hill, A.B., Han, R., Garcia, J.M., Bisio, H., Abergel, C., Kranzusch, P.J., Lee, A.S.Y.

(2026) Cell 189: 1423-1433.e16

• PubMed: 41709453 
• DOI: https://doi.org/10.1016/j.cell.2026.01.008
• Primary Citation Related Structures: 
  9E5A


• PubMed Abstract: 
  

  In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA viruses encode a distinct and functional IF4F translation-initiation complex to drive protein synthesis, thereby blurring the line between cellular and acellular biology. During infection, eukaryotic IF4F on host ribosomes is replaced by an essential viral IF4F that regulates viral translation, virion formation, and replication plasticity during altered host states. Structural dissection of viral IF4F reveals that the mRNA cap-binding subunit mediates exclusive interactions with viral mRNAs, constituting a molecular switch from translating host to viral proteins. Thus, our study establishes that viruses express a eukaryotic translation-initiation complex for protein synthesis, illuminating a series of evolutionary innovations in a core process of life.

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Organizational Affiliation: 
• Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Microbiology, Harvard Medical School, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256, IMM, IM2B, IOM, Marseille, France.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.9 kDa 
• Atom Count: 4,565 
• Modeled Residue Count: 501 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein R255	A, B	260	Acanthamoeba polyphaga mimivirus	Mutation(s): 0  Gene Names: MIMI_R255
UniProt
Find proteins for Q5UPT9 (Acanthamoeba polyphaga mimivirus) Explore Q5UPT9  Go to UniProtKB:  Q5UPT9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.654	α = 90
b = 91.317	β = 117.54
c = 58.529	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-25 
Deposition Author(s): Fels, J.M., Hill, A.B., Kranzusch, P.J., Lee, A.S.Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1DP2GM146250
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM142527

Revision History  

• Version 1.0: 2026-02-25
  Type: Initial release
  
• Version 1.1: 2026-09-09
  Changes: Database references