9CF5 | pdb_00009cf5

STRUCTURE OF CD4 MIMETIC CJF-III-288 IN COMPLEX WITH BG505 SOSIP.664 HIV-1ENV TRIMER AND 17B FAB


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CF5

This is version 1.1 of the entry. See complete history

Literature

The asymmetric opening of HIV-1 Env by a potent CD4 mimetic enables anti-coreceptor binding site antibodies to mediate ADCC.

Richard, J.Grunst, M.W.Niu, L.Diaz-Salinas, M.A.Tolbert, W.D.Marchitto, L.Zhou, F.Bourassa, C.Yang, D.Chiu, T.J.Chen, H.C.Benlarbi, M.Gottumukkala, S.Li, W.Dionne, K.Belanger, E.Chatterjee, D.Medjahed, H.Hendrickson, W.A.Sodroski, J.Lang, Z.C.Morton, A.J.Huang, R.K.Matthies, D.Smith 3rd, A.B.Mothes, W.Munro, J.B.Pazgier, M.Finzi, A.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.08.27.609961
  • Primary Citation Related Structures: 
    9CF5

  • PubMed Abstract: 

    HIV-1 envelope glycoproteins (Env) from primary HIV-1 isolates typically adopt a pretriggered "closed" conformation that resists to CD4-induced (CD4i) non-neutralizing antibodies (nnAbs) mediating antibody-dependent cellular cytotoxicity (ADCC). CD4-mimetic compounds (CD4mcs) "open-up" Env allowing binding of CD4i nnAbs, thereby sensitizing HIV-1-infected cells to ADCC. Two families of CD4i nnAbs, the anti-cluster A and anti-coreceptor binding site (CoRBS) Abs, are required to mediate ADCC in combination with the indane CD4mc BNM-III-170. Recently, new indoline CD4mcs with improved potency and breadth have been described. Here, we show that the lead indoline CD4mc, CJF-III-288, sensitizes HIV-1-infected cells to ADCC mediated by anti-CoRBS Abs alone, contributing to improved ADCC activity. Structural and conformational analyses reveal that CJF-III-288, in combination with anti-CoRBS Abs, potently stabilizes an asymmetric "open" State-3 Env conformation, This Env conformation orients the anti-CoRBS Ab to improve ADCC activity and therapeutic potential.


  • Organizational Affiliation
    • Centre de Recherche du CHUM, Montréal, Québec, Canada.

Macromolecule Content 

  • Total Structure Weight: 371.66 kDa 
  • Atom Count: 18,048 
  • Modeled Residue Count: 2,190 
  • Deposited Residue Count: 3,228 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A,
E [auth C],
I [auth E]
479Human immunodeficiency virus 1Mutation(s): 4 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 12
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41B,
F [auth D],
J [auth F]
153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
17b Fab light chainC [auth K],
G [auth I],
K [auth G]
214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
17b Fab heavy chainD [auth L],
H [auth J],
L [auth H]
230Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M,
O [auth W],
P [auth X],
R [auth P],
S [auth Q],
M,
O [auth W],
P [auth X],
R [auth P],
S [auth Q],
T [auth R],
V [auth T],
W [auth U],
X [auth V]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranose
N
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G56014GC
GlyCosmos: G56014GC
GlyGen: G56014GC
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-glucopyranoseQ [auth O],
U [auth S]
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G07617FP
GlyCosmos: G07617FP
GlyGen: G07617FP

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y26
(Subject of Investigation/LOI)

Query on Y26



Download:Ideal Coordinates CCD File
AB [auth E],
FA [auth A],
PA [auth C]
propyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate
C24 H29 Cl F N7 O4
YVEFINLMFLWNTD-UXHICEINSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
GA [auth B],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
QA [auth D],
RA [auth D],
SA [auth E],
TA [auth E],
UA [auth E],
VA [auth E],
WA [auth E],
XA [auth E],
Y [auth A],
YA [auth E],
Z [auth A],
ZA [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

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 StatesR01 AI174908
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI162242

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references