9CMT | pdb_00009cmt

The crystal structure of HP1alpha CSD-Agno complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 
    0.286 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 
    0.252 (Depositor) 

Starting Model: experimental
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Literature

Chromatin mimicry by human JC virus.

Schaefer, U.Miroshnikova, Y.A.Xie, W.Larson, A.G.Lu, Z.Chen, S.Bradic, M.Goldgur, Y.Chen, K.Sharma, V.P.Cao, J.Patel, D.J.Narlikar, G.J.Wickstrom, S.A.Tarakhovsky, A.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.11.04.621823
  • Primary Citation of Related Structures:  
    9CMT

  • PubMed Abstract: 

    Chronically persistent viruses are integral components of the organismal ecosystem in humans and animals 1 2 . Many of these viruses replicate and accumulate within the cell nucleus 3 . The nuclear location allows viruses to evade cytoplasmic host viral sensors and promotes viral replication 4 . One of the unexplored and puzzling aspects of the viral nuclear lifecycle involves the virus's ability to deal with the physical constraints of nuclear architecture. To replicate and accumulate within the nucleus in large numbers sufficient for infection spreading, DNA viruses need to overcome the spatial limitations imposed by chromatin and the nuclear matrix. We found that one of the most widespread and potentially lethal human viruses, the JC polyomavirus 5 , interferes with nuclear heterochromatin to create virus-occupied space. The JC virus's impact on heterochromatin is mediated by the viral nonstructural protein, Agnoprotein (Agno). Agno's interference with heterochromatin is governed by structurally diverse mimics of host epigenetic regulators that facilitate virus-induced chromatin reorganization and a dramatic decline in nuclear stiffness in the infected cells. The JCV epigenetic mimicry is critical for the virus infection, as evident from reduced replication of mimic-mutant viruses. Our data suggest that modulation of nuclear mechanical properties is a novel strategy enabling chronicity of the JC and possibly other nuclear virus infections.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromobox protein homolog 5
A, B, D, E
65Homo sapiensMutation(s): 2 
Gene Names: CBX5HP1A
UniProt & NIH Common Fund Data Resources
Find proteins for P45973 (Homo sapiens)
Explore P45973 
Go to UniProtKB:  P45973
PHAROS:  P45973
GTEx:  ENSG00000094916 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45973
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Agnoprotein
C, F
16JC polyomavirusMutation(s): 0 
UniProt
Find proteins for P03086 (JC polyomavirus)
Explore P03086 
Go to UniProtKB:  P03086
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03086
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F6Z
Query on F6Z

Download Ideal Coordinates CCD File 
G [auth C],
H [auth F]
3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-5-CARBOXYLIC ACID
C21 H12 O7
NJYVEMPWNAYQQN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free:  0.286 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 0.252 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.961α = 90
b = 112.961β = 90
c = 154.687γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM129430
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124165

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release