7SEP

Cryo-EM Structure of the RT component of the HIV-1 Pol Polyprotein

• PDB DOI: https://doi.org/10.2210/pdb7SEP/pdb
• EM Map EMD-25074: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 BH10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-10-01 Released: 2022-07-27 
• Deposition Author(s): Lyumkis, D., Passos, D., Arnold, E., Harrison, J.J.E.
• 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: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation.

Harrison, J.J.E.K., Passos, D.O., Bruhn, J.F., Bauman, J.D., Tuberty, L., DeStefano, J.J., Ruiz, F.X., Lyumkis, D., Arnold, E.

(2022) Sci Adv 8: eabn9874-eabn9874

• PubMed: 35857464 
• DOI: https://doi.org/10.1126/sciadv.abn9874
• Primary Citation of Related Structures:  
  7SEP, 7SJX


• PubMed Abstract: 
  

  Key proteins of retroviruses and other RNA viruses are translated and subsequently processed from polyprotein precursors by the viral protease (PR). Processing of the HIV Gag-Pol polyprotein yields the HIV structural proteins and enzymes. Structures of the mature enzymes PR, reverse transcriptase (RT), and integrase (IN) aided understanding of catalysis and design of antiretrovirals, but knowledge of the Pol precursor architecture and function before PR cleavage is limited. We developed a system to produce stable HIV-1 Pol and determined its cryo-electron microscopy structure. RT in Pol has a similar arrangement to the mature RT heterodimer, and its dimerization may draw together two PR monomers to activate proteolytic processing. HIV-1 thus may leverage the dimerization interfaces in Pol to regulate assembly and maturation of polyprotein precursors.

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Organizational Affiliation: 

Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 238.58 kDa 
• Atom Count: 7,641 
• Modelled Residue Count: 930 
• Deposited Residue Count: 2,106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag-Pol polyprotein	A, B	1,053	Human immunodeficiency virus type 1 BH10	Mutation(s): 3  Gene Names: gag-pol
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	RosettaEM
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Lyumkis, D., Passos, D., Arnold, E., Harrison, J.J.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)		R01 AI136680
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)		AI27690
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)		U54AI150472

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2022-08-03
  Changes: Database references