8PUH | pdb_00008puh

Structure of the immature HTLV-1 CA lattice from full-length Gag VLPs: CA-CTD refinement

• PDB DOI: https://doi.org/10.2210/pdb8PUH/pdb
• EM Map EMD-17943: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Human T-cell leukemia virus type I
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-07-17 Released: 2023-08-23 
• Deposition Author(s): Obr, M., Percipalle, M., Chernikova, D., Yang, H., Thader, A., Pinke, G., Porley, D., Mansky, L.M., Dick, R.A., Schur, F.K.M.
• Funding Organization(s): Austrian Science Fund, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Model: in silico

Literature

Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice.

Obr, M., Percipalle, M., Chernikova, D., Yang, H., Thader, A., Pinke, G., Porley, D., Mansky, L.M., Dick, R.A., Schur, F.K.M.

(2025) Nat Struct Mol Biol 32: 268-276

• PubMed: 39242978 
• DOI: https://doi.org/10.1038/s41594-024-01390-8
• Primary Citation Related Structures: 
  8PU6, 8PU7, 8PU8, 8PU9, 8PUA, 8PUB, 8PUC, 8PUD, 8PUE, 8PUF, 8PUG, 8PUH


• PubMed Abstract: 
  

  Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron tomography studies of HTLV-1 virus-like particles assembled in vitro, as well as derived from cells. This work shows that HTLV-1 uses a distinct mechanism of Gag-Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature capsid (CA) tubular arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal domain of CA. Mutagenesis analysis supports this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the C-terminal domain of CA. These results provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus and this helps explain why HTLV-1 particles are morphologically distinct.

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Organizational Affiliation: 
• Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
Material and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord, Eindhoven, Netherlands.
Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
Department of Pediatrics, Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Emory University School of Medicine, Atlanta, GA, USA.
Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria. [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: 95.11 kDa 
• Atom Count: 632 
• Modeled Residue Count: 158 
• Deposited Residue Count: 858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag polyprotein	A, B	429	Human T-cell leukemia virus type I	Mutation(s): 0  Gene Names: gag
UniProt
Find proteins for P03345 (Human T-cell leukemia virus 1 (strain Japan ATK-1 subtype A)) Explore P03345  Go to UniProtKB:  P03345

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	Warp	1.0.9

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Obr, M., Percipalle, M., Chernikova, D., Yang, H., Thader, A., Pinke, G., Porley, D., Mansky, L.M., Dick, R.A., Schur, F.K.M.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P31445
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 GM151775
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21 DE032878
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI147890

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release
  
• Version 1.1: 2024-09-11
  Changes: Data collection, Database references
• Version 1.2: 2024-09-18
  Changes: Data collection, Database references
• Version 1.3: 2025-02-26
  Changes: Data collection, Database references, Structure summary