9N92 | pdb_00009n92

High-resolution analysis of the human T-cell leukemia virus capsid protein reveals insights into immature particle morphology

• PDB DOI: https://doi.org/10.2210/pdb9N92/pdb
• EM Map EMD-48796: EMDB EMDataResource

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


• Deposited: 2025-02-10 Released: 2025-12-24 
• Deposition Author(s): Arndt, W.G., Ramezani, A., Talledge, N., Yu, G., Yang, H., Chen, B., Zhang, W., Mansky, L.M., Perilla, J.R.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.44 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

High-resolution analysis of the human T-cell leukemia virus capsid protein reveals insights into immature particle morphology.

Arndt, W.G., Ramezani, A., Talledge, N., Yu, G., Yang, H., Chen, B., Perilla, J.R., Zhang, W., Mansky, L.M.

(2025) Nat Commun 

• PubMed: 41381513 
• DOI: https://doi.org/10.1038/s41467-025-67129-1
• Primary Citation of Related Structures:  
  9N0W, 9N92


• PubMed Abstract: 
  

  Infection with human T-cell leukemia virus type 1 (HTLV-1) can result in adult T-cell leukemia/lymphoma and HTLV-1 associated-myelopathy/tropical spastic paraparesis. The Gag polyprotein - the major structural protein - is crucial for driving virus particle assembly, with the capsid (CA) domain as the key determinant for Gag multimerization. Here, we characterize the immature CA lattice from immature virus particles by using cryo-electron microscopy and tomography (cryo-EM/ET). We report resolving the immature CA lattice to 3.4 Å resolution by single particle analysis (SPA). Our reconstruction reveals that the lattice is stabilized through a trimeric NTD inter-hexamer interface and a dimeric CTD inter-hexamer interface. Further analysis by cryo-ET reveals clear heterogeneity, notably the varying lattice curvatures and the varying distances from the CA layer to the membrane. Intriguingly, inositol hexakisphosphate (IP6) is dispensable for HTLV-1 immature particle assembly and proper immature lattice formation. These observations provide deeper insights into the molecular basis of HTLV-1 immature particle morphology as well as aid in revealing therapeutic targets.

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Organizational Affiliation: 
• Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
Institute for Molecular Virology, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
Department of Diagnostic & Biological Sciences, School of Dentistry, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
Masonic Cancer Center, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
Department of Chemistry & Biochemistry, University of Delaware, Newark, DE, USA.
Minnesota Supercomputing Institute, Office of the Vice President for Research, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
Characterization Facility, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
Department of Physics, University of Central Florida, Orlando, FL, USA.
Institute for Molecular Virology, University of Minnesota-Twin Cities, Minneapolis, MN, USA. [e-mail].
Department of Diagnostic & Biological Sciences, School of Dentistry, University of Minnesota-Twin Cities, Minneapolis, MN, USA. [e-mail].
Masonic Cancer Center, University of Minnesota-Twin Cities, Minneapolis, MN, USA. [e-mail].
Characterization Facility, University of Minnesota-Twin Cities, Minneapolis, MN, USA. [e-mail].
Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA. [e-mail].
Institute for Molecular Virology, University of Minnesota-Twin Cities, Minneapolis, MN, USA. [e-mail].
Department of Diagnostic & Biological Sciences, School of Dentistry, University of Minnesota-Twin Cities, Minneapolis, MN, USA. [e-mail].
Masonic Cancer Center, University of Minnesota-Twin Cities, Minneapolis, MN, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 18-mer - A18 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 391.07 kDa 
• Atom Count: 27,486 
• Modeled Residue Count: 3,510 
• Deposited Residue Count: 3,510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag protein	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	195	Human T-cell leukemia virus type I	Mutation(s): 0  Gene Names: gag
UniProt
Find proteins for Q82230 (Human T-cell leukemia virus type I) Explore Q82230  Go to UniProtKB:  Q82230

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP (Subject of Investigation/LOI)	S [auth E]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.44 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5.0b-3_cu11.8
MODEL REFINEMENT	MDFF

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Arndt, W.G., Ramezani, A., Talledge, N., Yu, G., Yang, H., Chen, B., Zhang, W., Mansky, L.M., Perilla, J.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI178846
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54AI170791
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01GM151775
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21DE032878
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	F31AI184673
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32AI083196
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32DA007097
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	F32AI150351

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release