6R2G

Crystal structure of a single-chain protein mimetic of the gp41 NHR trimer in complex with the synthetic CHR peptide C34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Thermodynamic Analysis of HIV-1 Fusion Inhibition Using Small gp41 Mimetic Proteins.

Jurado, S.Cano-Munoz, M.Morel, B.Standoli, S.Santarossa, E.Moog, C.Schmidt, S.Laumond, G.Camara-Artigas, A.Conejero-Lara, F.

(2019) J Mol Biol 431: 3091-3106

  • DOI: 10.1016/j.jmb.2019.06.022
  • Primary Citation of Related Structures:  
    6R2G

  • PubMed Abstract: 
  • Development of effective inhibitors of the fusion between HIV-1 and the host cell membrane mediated by gp41 continues to be a grand challenge due to an incomplete understanding of the molecular and mechanistic details of the fusion process. We previously developed single-chain, chimeric proteins (named covNHR) that accurately mimic the N-heptad repeat (NHR) region of gp41 in a highly stable coiled-coil conformation ...

    Development of effective inhibitors of the fusion between HIV-1 and the host cell membrane mediated by gp41 continues to be a grand challenge due to an incomplete understanding of the molecular and mechanistic details of the fusion process. We previously developed single-chain, chimeric proteins (named covNHR) that accurately mimic the N-heptad repeat (NHR) region of gp41 in a highly stable coiled-coil conformation. These molecules bind strongly to peptides derived from the gp41 C-heptad repeat (CHR) and are potent and broad HIV-1 inhibitors. Here, we investigated two covNHR variants differing in two mutations, V10E and Q123R (equivalent to V38E and Q40R in gp41 sequence) that reproduce the effect of HIV-1 mutations associated with resistance to fusion inhibitors, such as T20 (enfuvirtide). A detailed calorimetric analysis of the binding between the covNHR proteins and CHR peptides (C34 and T20) reveals drastic changes in affinity due to the mutations as a result of local changes in interactions at the site of T20 resistance. The crystallographic structure of the covNHR:C34 complex shows a virtually identical CHR-NHR binding interface to that of the post-fusion structure of gp41 and underlines an important role of buried interfacial water molecules in binding affinity and in development of resistance against CHR peptides. Despite the great difference in affinity, both covNHR variants demonstrate strong inhibitory activity for a wide variety of HIV-1 strains. These properties support the high potential of these covNHR proteins as new potent HIV-1 inhibitors. Our results may guide future inhibition approaches.


    Related Citations: 
    • Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41 with potential as anti-HIV-1 drugs.
      Crespillo, S., Camara-Artigas, A., Casares, S., Morel, B., Cobos, E.S., Mateo, P.L., Mouz, N., Martin, C.E., Roger, M.G., El Habib, R., Su, B., Moog, C., Conejero-Lara, F.
      (2014) Proc Natl Acad Sci U S A 111: 18207

    Organizational Affiliation

    Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain. Electronic address: conejero@ugr.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41A182Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P03377 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03377 
Go to UniProtKB:  P03377
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03377
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160B [auth C]36Human immunodeficiency virus type 1 (BRU ISOLATE)Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for P03377 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03377 
Go to UniProtKB:  P03377
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03377
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.201α = 90
b = 69.664β = 90
c = 95.836γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBIO2016-76640-R
Spanish Ministry of Economy and CompetitivenessSpainBIO2016-78020-R

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Database references