8TTW

Cryo-EM structure of BG505 SOSIP.664 HIV-1 Env trimer in complex with temsavir, 8ANC195, and 10-1074


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 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

Structure-function analyses reveal key molecular determinants of HIV-1 CRF01_AE resistance to the entry inhibitor temsavir.

Prevost, J.Chen, Y.Zhou, F.Tolbert, W.D.Gasser, R.Medjahed, H.Nayrac, M.Nguyen, D.N.Gottumukkala, S.Hessell, A.J.Rao, V.B.Pozharski, E.Huang, R.K.Matthies, D.Finzi, A.Pazgier, M.

(2023) Nat Commun 14: 6710-6710

  • DOI: https://doi.org/10.1038/s41467-023-42500-2
  • Primary Citation of Related Structures:  
    8CZZ, 8DOK, 8G6U, 8TTW

  • PubMed Abstract: 

    The HIV-1 entry inhibitor temsavir prevents the viral receptor CD4 (cluster of differentiation 4) from interacting with the envelope glycoprotein (Env) and blocks its conformational changes. To do this, temsavir relies on the presence of a residue with small side chain at position 375 in Env and is unable to neutralize viral strains like CRF01_AE carrying His375. Here we investigate the mechanism of temsavir resistance and show that residue 375 is not the sole determinant of resistance. At least six additional residues within the gp120 inner domain layers, including five distant from the drug-binding pocket, contribute to resistance. A detailed structure-function analysis using engineered viruses and soluble trimer variants reveals that the molecular basis of resistance is mediated by crosstalk between His375 and the inner domain layers. Furthermore, our data confirm that temsavir can adjust its binding mode to accommodate changes in Env conformation, a property that likely contributes to its broad antiviral activity.


  • Organizational Affiliation

    Centre de Recherche du CHUM, Montreal, QC, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160
A, E, I
481Human immunodeficiency virus 1Mutation(s): 6 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BG505 SOSIP.664 transmembrane protein gp41
B, F, J
153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus 1)
Explore Q2N0S5 
Go to UniProtKB:  Q2N0S5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 8anc195 heavy chain
C, G, K
238Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 8anc195 light chain
D, H, L
215Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 10-1074 heavy chain
M, O, Q
238Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 10-1074 light chain
N, P, R
214Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BB [auth 1],
CB [auth 2],
DA [auth d],
EA [auth e],
AA [auth a],
BB [auth 1],
CB [auth 2],
DA [auth d],
EA [auth e],
EB [auth 4],
FB [auth 5],
GA [auth g],
GB [auth 6],
HA [auth h],
HB [auth 7],
IA [auth i],
JA [auth j],
KA [auth k],
LA [auth l],
MA [auth m],
PA [auth p],
QA [auth q],
S,
SA [auth s],
T,
TA [auth t],
U,
UA [auth u],
V,
VA [auth v],
W,
WA [auth w],
X,
XA [auth x],
Y,
YA [auth y],
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBA [auth b],
NA [auth n],
ZA [auth z]
10N-Glycosylation
Glycosylation Resources
GlyTouCan:  G40702WU
GlyCosmos:  G40702WU
GlyGen:  G40702WU
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAB [auth 0],
CA [auth c],
OA [auth o]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseDB [auth 3],
FA [auth f],
RA [auth r]
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68668TB
GlyCosmos:  G68668TB
GlyGen:  G68668TB
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
83J (Subject of Investigation/LOI)
Query on 83J

Download Ideal Coordinates CCD File 
CC [auth I],
MB [auth A],
UB [auth E]
1-[4-(benzenecarbonyl)piperazin-1-yl]-2-[4-methoxy-7-(3-methyl-1H-1,2,4-triazol-1-yl)-1H-pyrrolo[2,3-c]pyridin-3-yl]ethane-1,2-dione
C24 H23 N7 O4
QRPZBKAMSFHVRW-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AC [auth I]
BC [auth I]
DC [auth J]
EC [auth J]
FC [auth K]
AC [auth I],
BC [auth I],
DC [auth J],
EC [auth J],
FC [auth K],
IB [auth A],
JB [auth A],
KB [auth A],
LB [auth A],
NB [auth B],
OB [auth B],
PB [auth C],
QB [auth E],
RB [auth E],
SB [auth E],
TB [auth E],
VB [auth F],
WB [auth F],
XB [auth G],
YB [auth I],
ZB [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI120756
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI174908

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release