7U32

MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Multivalent interactions essential for lentiviral integrase function.

Ballandras-Colas, A., Chivukula, V., Gruszka, D.T., Shan, Z., Singh, P.K., Pye, V.E., McLean, R.K., Bedwell, G.J., Li, W., Nans, A., Cook, N.J., Fadel, H.J., Poeschla, E.M., Griffiths, D.J., Vargas, J., Taylor, I.A., Lyumkis, D., Yardimci, H., Engelman, A.N., Cherepanov, P.

(2022) Nat Commun 13: 2416-2416

  • DOI: 10.1038/s41467-022-29928-8
  • Primary Citation of Related Structures:  
    7U32

  • PubMed Abstract: 

    • A multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of the intasome from the maedi-visna virus (MVV), an ovine lentivirus, revealed a large assembly containing sixteen IN subunits 1 ...

    A multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of the intasome from the maedi-visna virus (MVV), an ovine lentivirus, revealed a large assembly containing sixteen IN subunits 1 . Herein, we report cryo-EM structures of the lentiviral intasome prior to engagement of target DNA and following strand transfer, refined at 3.4 and 3.5 Å resolution, respectively. The structures elucidate details of the protein-protein and protein-DNA interfaces involved in lentiviral intasome formation. We show that the homomeric interfaces involved in IN hexadecamer formation and the α-helical configuration of the linker connecting the C-terminal and catalytic core domains are critical for MVV IN strand transfer activity in vitro and for virus infectivity. Single-molecule microscopy in conjunction with photobleaching reveals that the MVV intasome can bind a variable number, up to sixteen molecules, of the lentivirus-specific host factor LEDGF/p75. Concordantly, ablation of endogenous LEDGF/p75 results in gross redistribution of MVV integration sites in human and ovine cells. Our data confirm the importance of the expanded architecture observed in cryo-EM studies of lentiviral intasomes and suggest that this organization underlies multivalent interactions with chromatin for integration targeting to active genes.

    Organizational Affiliation: 

    Department of Infectious Disease, St-Mary's Campus, Imperial College London, London, UK. Peter.Cherepanov@crick.ac.uk.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integrase
A,
B,
C,
D,
E,
281Visna/maedi virus EV1 KV1772Mutation(s): 0 
Gene Names: pol
EC: 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data), 3.4.23 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.4 (UniProt), 3.1.13.2 (UniProt), 3.6.1.23 (UniProt)
UniProt
Find proteins for P35956 (Maedi visna virus (strain KV1772))
Explore P35956 
Go to UniProtKB:  P35956
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35956
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA EV273I [auth X],
S [auth Y]		29synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA EV272J [auth W],
T [auth Z]		27synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

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
The Francis Crick InstituteUnited KingdomFC10061
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP50AI150481

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release