7JN3 | pdb_00007jn3

Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048

• PDB DOI: https://doi.org/10.2210/pdb7JN3/pdb
• NAKB: 7JN3
• EM Map EMD-22400: EMDB EMDataResource

• Classification: HYDROLASE/DNA/INHIBITOR
• Organism(s): Rous sarcoma virus (strain Schmidt-Ruppin A)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-08-03 Released: 2021-03-17 
• Deposition Author(s): Pandey, K.K., Bera, S., Shi, K., Aihara, H., Grandgenett, D.P.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome.

Pandey, K.K., Bera, S., Shi, K., Rau, M.J., Oleru, A.V., Fitzpatrick, J.A.J., Engelman, A.N., Aihara, H., Grandgenett, D.P.

(2021) Commun Biol 4: 330-330

• PubMed: 33712691 
• DOI: https://doi.org/10.1038/s42003-021-01855-2
• Primary Citation Related Structures: 
  7JN3, 7KU7, 7KUI


• PubMed Abstract: 
  

  Despite conserved catalytic integration mechanisms, retroviral intasomes composed of integrase (IN) and viral DNA possess diverse structures with variable numbers of IN subunits. To investigate intasome assembly mechanisms, we employed the Rous sarcoma virus (RSV) IN dimer that assembles a precursor tetrameric structure in transit to the mature octameric intasome. We determined the structure of RSV octameric intasome stabilized by a HIV-1 IN strand transfer inhibitor using single particle cryo-electron microscopy. The structure revealed significant flexibility of the two non-catalytic distal IN dimers along with previously unrecognized movement of the conserved intasome core, suggesting ordered conformational transitions between intermediates that may be important to capture the target DNA. Single amino acid substitutions within the IN C-terminal domain affected intasome assembly and function in vitro and infectivity of pseudotyped RSV virions. Unexpectedly, 17 C-terminal amino acids of IN were dispensable for virus infection despite regulating the transition of the tetrameric intasome to the octameric form in vitro. We speculate that this region may regulate the binding of highly flexible distal IN dimers to the intasome core to form the octameric complex. Our studies reveal key steps in the assembly of RSV intasomes.

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Organizational Affiliation: 
• Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO, USA. [e-mail].
Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO, USA.
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA.
Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
Departments of Cell Biology & Physiology and Neuroscience, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.
Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
Department of Medicine, Harvard Medical School, Boston, MA, USA.
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA. [e-mail].
Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 8-mer - A8 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 269.4 kDa 
• Atom Count: 15,666 
• Modeled Residue Count: 1,875 
• Deposited Residue Count: 2,292 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
integrase	A, B, C, D, E, F, G, H	278	Rous sarcoma virus (strain Schmidt-Ruppin A)	Mutation(s): 1  EC: 3.4.23 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P03354 (Rous sarcoma virus subgroup C (strain Prague)) Explore P03354  Go to UniProtKB:  P03354

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*T)-3')	I, K	18	Rous sarcoma virus (strain Schmidt-Ruppin A)

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*GP*CP*AP*TP*AP*AP*GP*AP*CP*AP*AP*CP*A)-3')	J, L	16	Rous sarcoma virus (strain Schmidt-Ruppin A)

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZZX	N [auth A], R [auth E]	(6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide C21 H21 Cl F N5 O4 JSRREMIKIHJGAA-JTQLQIEISA-N
ZN	M [auth A], Q [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	O [auth A], P [auth A], S [auth E], T [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Pandey, K.K., Bera, S., Shi, K., Aihara, H., Grandgenett, D.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI127196
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2021-10-06
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Refinement description