4U7Q

Structure of wild-type HIV protease in complex with photosensitive inhibitor PDI-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.275 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Triggering HIV polyprotein processing by light using rapid photodegradation of a tight-binding protease inhibitor.

Schimer, J.Pavova, M.Anders, M.Pachl, P.Sacha, P.Cigler, P.Weber, J.Majer, P.Rezacova, P.Krausslich, H.G.Muller, B.Konvalinka, J.

(2015) Nat Commun 6: 6461-6461

  • DOI: 10.1038/ncomms7461
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HIV protease (PR) is required for proteolytic maturation in the late phase of HIV replication and represents a prime therapeutic target. The regulation and kinetics of viral polyprotein processing and maturation are currently not understood in detail ...

    HIV protease (PR) is required for proteolytic maturation in the late phase of HIV replication and represents a prime therapeutic target. The regulation and kinetics of viral polyprotein processing and maturation are currently not understood in detail. Here we design, synthesize, validate and apply a potent, photodegradable HIV PR inhibitor to achieve synchronized induction of proteolysis. The compound exhibits subnanomolar inhibition in vitro. Its photolabile moiety is released on light irradiation, reducing the inhibitory potential by 4 orders of magnitude. We determine the structure of the PR-inhibitor complex, analyze its photolytic products, and show that the enzymatic activity of inhibited PR can be fully restored on inhibitor photolysis. We also demonstrate that proteolysis of immature HIV particles produced in the presence of the inhibitor can be rapidly triggered by light enabling thus to analyze the timing, regulation and spatial requirements of viral processing in real time.


    Organizational Affiliation

    Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.,1] Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic [2] Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague 2, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic.,1] Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany [2] Molecular Medicine Partnership Unit, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-1 protease
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3EM
Query on 3EM

Download SDF File 
Download CCD File 
B
N~2~-({[7-(diethylamino)-2-oxo-2H-chromen-4-yl]methoxy}carbonyl)-N-[(2S,4S,5S)-4-hydroxy-1,6-diphenyl-5-{[(1,3-thiazol-5-ylmethoxy)carbonyl]amino}hexan-2-yl]-L-valinamide
C43 H51 N5 O8 S
HWKZGVMRBIGKNW-FUVWEXRVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3EMKi: 0.18 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.275 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.841α = 90.00
b = 62.841β = 90.00
c = 80.486γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
MOLREPphasing
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education of the CzechRepublicCzech RepublicP208-12-G016
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLO 1302
German Research FoundationGermanyMU885/5-1

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 2.0: 2017-09-06
    Type: Atomic model, Author supporting evidence, Derived calculations, Refinement description