6BEE

Crystal structure of VACV D13 in complex with Rifaximin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin.

Garriga, D.Headey, S.Accurso, C.Gunzburg, M.Scanlon, M.Coulibaly, F.

(2018) Proc Natl Acad Sci U S A 115: 8424-8429

  • DOI: 10.1073/pnas.1810398115
  • Primary Citation of Related Structures:  
    6BEI, 6BEB, 6BED, 6BEC, 6BEF, 6BEE, 6BEH, 6BEG

  • PubMed Abstract: 
  • Poxviruses are large DNA viruses that cause disease in animals and humans. They differ from classical enveloped viruses, because their membrane is acquired from cytoplasmic membrane precursors assembled onto a viral protein scaffold formed by the D13 protein rather than budding through cellular compartments ...

    Poxviruses are large DNA viruses that cause disease in animals and humans. They differ from classical enveloped viruses, because their membrane is acquired from cytoplasmic membrane precursors assembled onto a viral protein scaffold formed by the D13 protein rather than budding through cellular compartments. It was found three decades ago that the antibiotic rifampicin blocks this process and prevents scaffold formation. To elucidate the mechanism of action of rifampicin, we have determined the crystal structures of six D13-rifamycin complexes. These structures reveal that rifamycin compounds bind to a phenylalanine-rich region, or F-ring, at the membrane-proximal opening of the central channel of the D13 trimer. We show by NMR, surface plasmon resonance (SPR), and site-directed mutagenesis that A17, a membrane-associated viral protein, mediates the recruitment of the D13 scaffold by also binding to the F-ring. This interaction is the target of rifampicin, which prevents A17 binding, explaining the inhibition of viral morphogenesis. The F-ring of D13 is both conserved in sequence in mammalian poxviruses and essential for interaction with A17, defining a target for the development of assembly inhibitors. The model of the A17-D13 interaction describes a two-component system for remodeling nascent membranes that may be conserved in other large and giant DNA viruses.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Scaffold protein D13A, B, C553Vaccinia virus WRMutation(s): 0 
Gene Names: VACWR118D13L
UniProt
Find proteins for P68440 (Vaccinia virus (strain Western Reserve))
Explore P68440 
Go to UniProtKB:  P68440
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RXM
Query on RXM

Download Ideal Coordinates CCD File 
G [auth B](2S,16Z,18E,20S,21S,22R,23R,24R,25S,26R,27S,28E)-5,6,21,23-tetrahydroxy-27-methoxy-2,4,11,16,20,22,24,26-octamethyl-1,1 5-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)furo[2'',3'':7',8']naphtho[1',2':4,5]imidazo[1,2-a]pyridin-2 5-yl acetate
C43 H51 N3 O11
NZCRJKRKKOLAOJ-XRCRFVBUSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], I [auth B], M [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
D [auth A], H [auth B], J [auth C], K [auth C], L [auth C]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.14α = 90
b = 191.14β = 90
c = 253.27γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1051907

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.3: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.4: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2020-01-08
    Changes: Author supporting evidence