8Z7N | pdb_00008z7n

Structure of HIV-1 CH119 SOSIP.664 trimer in complex with CD4 molecules


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Intermediate open state of CD4-bound HIV-1 env heterotrimers in asia CRFs.

Li, D.Liu, L.Ye, X.Chen, Y.Ren, Q.Xu, S.Ren, Y.Cao, H.Wang, T.

(2024) Biochem Biophys Res Commun 725: 150249-150249

  • DOI: https://doi.org/10.1016/j.bbrc.2024.150249
  • Primary Citation of Related Structures:  
    8Z7N

  • PubMed Abstract: 

    The HIV-1 envelope glycoprotein (Env) plays crucial role in viral infection by facilitating viral attachment to host cells and inducing fusion of the virus with the host cell membrane. This fusion allows the HIV-1 viral genome to enter the target cell then triggering various stages of the viral life cycle. The native Env directly interacts with the main receptor CD4 and the co-receptor (CCR5 or CXCR4) in human cell membrane then induces membrane fusion. The elucidation of the structure of Env with CD4 and co-receptors in different HIV-1 subtypes is essential for the understanding of the mechanism of virus entry. Here we report the Cryo-EM structure of the CD4-bound HIV-1 heterotrimeric Env from Asia prevalent CRF07_BC CH119 strain. In this structure, the binding of three CD4 molecules with Env induced extensively conformational changes in gp120, resulting in the transformation of the Env from close state to intermediate open state. Additionally, the conformational shift of V1/V2 loops of the heterotrimeric Env allosterically expose the V3 loop and promoting the further interactions with co-receptor CCR5 or CXCR4. These findings not only illustrate the structural complexity and plasticity of HIV-1 Env but also give new insights how the biological trimeric Env initialize the immune recognition and membrane fusion.


  • Organizational Affiliation
    • School of basic medical Sciences, Capital Medical University, 10 Xitoutiao You'anMen Street, Beijing, 100069, China; Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160
A, D, G
518Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
UniProt
Find proteins for A1EAH4 (Human immunodeficiency virus type 1)
Explore A1EAH4 
Go to UniProtKB:  A1EAH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1EAH4
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160
B, E, H
164Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for A1EAH4 (Human immunodeficiency virus type 1)
Explore A1EAH4 
Go to UniProtKB:  A1EAH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1EAH4
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD4
C, F, I
401Homo sapiensMutation(s): 0 
Gene Names: CD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens)
Explore P01730 
Go to UniProtKB:  P01730
PHAROS:  P01730
GTEx:  ENSG00000010610 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01730
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth H]
J [auth A]
K [auth A]
L [auth B]
M [auth B]
AA [auth H],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth D],
Q [auth D],
R [auth E],
S [auth E],
T [auth E],
U [auth E],
V [auth G],
W [auth G],
X [auth H],
Y [auth H],
Z [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedChina--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-11-27
    Changes: Data collection
  • Version 1.3: 2025-04-23
    Changes: Data collection, Database references