6VOY | pdb_00006voy

Cryo-EM structure of HTLV-1 instasome

• PDB DOI: https://doi.org/10.2210/pdb6VOY/pdb
• NAKB: 6VOY
• EM Map EMD-21301: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Saccharolobus solfataricus P2, Human T-cell leukemia virus type I, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-02-01 Released: 2020-07-01 
• Deposition Author(s): Bhatt, V., Shi, K., Sundborger, A., Aihara, H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of host protein hijacking in human T-cell leukemia virus integration.

Bhatt, V., Shi, K., Salamango, D.J., Moeller, N.H., Pandey, K.K., Bera, S., Bohl, T.E., Kurniawan, F., Orellana, K., Zhang, W., Grandgenett, D.P., Harris, R.S., Sundborger-Lunna, A.C., Aihara, H.

(2020) Nat Commun 11: 3121-3121

• PubMed: 32561747 
• DOI: https://doi.org/10.1038/s41467-020-16963-6
• Primary Citation Related Structures: 
  6VOY


• PubMed Abstract: 
  

  Integration of the reverse-transcribed viral DNA into host chromosomes is a critical step in the life-cycle of retroviruses, including an oncogenic delta(δ)-retrovirus human T-cell leukemia virus type-1 (HTLV-1). Retroviral integrase forms a higher order nucleoprotein assembly (intasome) to catalyze the integration reaction, in which the roles of host factors remain poorly understood. Here, we use cryo-electron microscopy to visualize the HTLV-1 intasome at 3.7-Å resolution. The structure together with functional analyses reveal that the B56γ (B'γ) subunit of an essential host enzyme, protein phosphatase 2 A (PP2A), is repurposed as an integral component of the intasome to mediate HTLV-1 integration. Our studies reveal a key host-virus interaction underlying the replication of an important human pathogen and highlight divergent integration strategies of retroviruses.

---

Organizational Affiliation: 
• The Hormel Institute, University of Minnesota, 801 16th Avenue N.E., Austin, MN, 55912, USA.
Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA.
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA.
Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA.
Department of Molecular Microbiology and Immunology, Saint Louis University, 1100 S. Grand Boulevard, St. Louis, MO, 63104, USA.
Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA.
Characterization Facility, College of Science and Engineering, University of Minnesota, 100 Union Street S.E., Minneapolis, MN, 55455, USA.
Howard Hughes Medical Institute, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA.
The Hormel Institute, University of Minnesota, 801 16th Avenue N.E., Austin, MN, 55912, USA. [e-mail].
Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA. [e-mail].
Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA. [e-mail].
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA. [e-mail].
Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 313.41 kDa 
• Atom Count: 17,556 
• Modeled Residue Count: 1,904 
• Deposited Residue Count: 2,434 
• Unique protein chains: 2
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein 7d	A, B, C, D	390	Saccharolobus solfataricus P2, Human T-cell leukemia virus type I This entity is chimeric	Mutation(s): 1  Gene Names: sso7d, sso7d-1, SSO10610, pol
UniProt
Find proteins for P14078 (Human T-cell leukemia virus 1 (isolate Caribbea HS-35 subtype A)) Explore P14078  Go to UniProtKB:  P14078
Find proteins for P39476 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore P39476  Go to UniProtKB:  P39476
UniProt Groups	P14078P39476

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform	E, F	343	Homo sapiens	Mutation(s): 0  Gene Names: PPP2R5C, KIAA0044
UniProt & NIH Common Fund Data Resources
Find proteins for Q13362 (Homo sapiens) Explore Q13362  Go to UniProtKB:  Q13362
PHAROS:  Q13362 GTEx:  ENSG00000078304

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')	G [auth I], J [auth L]	49	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	H [auth J], K [auth M]	25	Human T-cell leukemia virus type I

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')	I [auth K], L [auth N]	20	Human T-cell leukemia virus type I

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	M [auth A], O [auth B], P [auth C], R [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	N [auth A], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.08

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Bhatt, V., Shi, K., Sundborger, A., Aihara, H.

---

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

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2025-05-28
  Changes: Data collection