8CZZ

Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS mutations in complex with Temsavir, 8ANC195, and 10-1074


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
CRF01_AE T/F100 HIV-1 gp120
A, E, I
486Human immunodeficiency virus 1Mutation(s): 6 
Gene Names: env
UniProt
Find proteins for A0A140EMT3 (Human immunodeficiency virus 1)
Explore A0A140EMT3 
Go to UniProtKB:  A0A140EMT3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140EMT3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRF-1_AE T/F100 HIV-1 gp41
B, F, J
155Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for A0A2R8G1F7 (Human immunodeficiency virus 1)
Explore A0A2R8G1F7 
Go to UniProtKB:  A0A2R8G1F7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2R8G1F7
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of 8ANC195 Fab
C, G, K
238Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of 8ANC195 Fab
D, H, L
215Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of 10-1074 Fab
M, O, Q
238Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of 10-1074 Fab
N, P, R
214Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 7
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-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJA [auth j],
S
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G04414GO
GlyCosmos:  G04414GO
GlyGen:  G04414GO
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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],
KA [auth k],
T
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseDA [auth d],
NA [auth n],
U
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G01361SX
GlyCosmos:  G01361SX
GlyGen:  G01361SX
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
CA [auth c],
EA [auth e],
FA [auth f],
GA [auth g],
LA [auth l],
CA [auth c],
EA [auth e],
FA [auth f],
GA [auth g],
LA [auth l],
MA [auth m],
OA [auth o],
PA [auth p],
QA [auth q],
V,
W,
X
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseHA [auth h],
IA [auth i],
RA [auth r],
Y,
Z
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 12
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-glucopyranoseAA [auth a]10N-Glycosylation
Glycosylation Resources
GlyTouCan:  G40702WU
GlyCosmos:  G40702WU
GlyGen:  G40702WU
Entity ID: 13
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseSA [auth s]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
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 
LB [auth E],
TA [auth A],
YB [auth I]
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 
AB [auth A]
AC [auth J]
BB [auth A]
BC [auth J]
CB [auth B]
AB [auth A],
AC [auth J],
BB [auth A],
BC [auth J],
CB [auth B],
CC [auth J],
DB [auth B],
DC [auth K],
EB [auth C],
FB [auth E],
GB [auth E],
HB [auth E],
IB [auth E],
JB [auth E],
KB [auth E],
MB [auth E],
NB [auth E],
OB [auth F],
PB [auth F],
QB [auth F],
RB [auth G],
SB [auth I],
TB [auth I],
UA [auth A],
UB [auth I],
VA [auth A],
VB [auth I],
WA [auth A],
WB [auth I],
XA [auth A],
XB [auth I],
YA [auth A],
ZA [auth A],
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: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited StatesStart-up funds

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description