7USF

Mouse mammary tumor virus strand transfer complex intasome

  • Classification: HYDROLASE/DNA
  • Organism(s): Mouse mammary tumor virus
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2022-04-25 Released: 2022-08-24 
  • Deposition Author(s): Jozwik, I., Lyumkis, D.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

B-to-A transition in target DNA during retroviral integration.

Jozwik, I.K.Li, W.Zhang, D.W.Wong, D.Grawenhoff, J.Ballandras-Colas, A.Aiyer, S.Cherepanov, P.Engelman, A.N.Lyumkis, D.

(2022) Nucleic Acids Res 50: 8898-8918

  • DOI: https://doi.org/10.1093/nar/gkac644
  • Primary Citation of Related Structures:  
    7USF, 7UT1

  • PubMed Abstract: 

    Integration into host target DNA (tDNA), a hallmark of retroviral replication, is mediated by the intasome, a multimer of integrase (IN) assembled on viral DNA (vDNA) ends. To ascertain aspects of tDNA recognition during integration, we have solved the 3.5 Å resolution cryo-EM structure of the mouse mammary tumor virus (MMTV) strand transfer complex (STC) intasome. The tDNA adopts an A-like conformation in the region encompassing the sites of vDNA joining, which exposes the sugar-phosphate backbone for IN-mediated strand transfer. Examination of existing retroviral STC structures revealed conservation of A-form tDNA in the analogous regions of these complexes. Furthermore, analyses of sequence preferences in genomic integration sites selectively targeted by six different retroviruses highlighted consistent propensity for A-philic sequences at the sites of vDNA joining. Our structure additionally revealed several novel MMTV IN-DNA interactions, as well as contacts seen in prior STC structures, including conserved Pro125 and Tyr149 residues interacting with tDNA. In infected cells, Pro125 substitutions impacted the global pattern of MMTV integration without significantly altering local base sequence preferences at vDNA insertion sites. Collectively, these data advance our understanding of retroviral intasome structure and function, as well as factors that influence patterns of vDNA integration in genomic DNA.


  • Organizational Affiliation

    The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrase
A, B, C, D
319Mouse mammary tumor virusMutation(s): 1 
Gene Names: gag-pro-pol
UniProt
Find proteins for P03365 (Mouse mammary tumor virus (strain BR6))
Explore P03365 
Go to UniProtKB:  P03365
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03365
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
vDNA strand (non-transferred)E [auth I]30Mouse mammary tumor virus
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
vDNA-tDNA strand (transferred)F [auth J]42Mouse mammary tumor virus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
tDNA strandG [auth K]16Mouse mammary tumor virus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.0
MODEL REFINEMENTCoot

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-2048095
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU54 AI150472
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI136680

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2024-06-12
    Changes: Data collection