8GP5 | pdb_00008gp5

Structure of X18 UFO protomer in complex with F6 Fab VHVL domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8GP5

This is version 1.3 of the entry. See complete history

Literature

Structures and immune recognition of Env trimers from two Asia prevalent HIV-1 CRFs.

Niu, J.Wang, Q.Zhao, W.Meng, B.Xu, Y.Zhang, X.Feng, Y.Qi, Q.Hao, Y.Zhang, X.Liu, Y.Xiang, J.Shao, Y.Yang, B.

(2023) Nat Commun 14: 4676-4676

  • DOI: https://doi.org/10.1038/s41467-023-40321-x
  • Primary Citation Related Structures: 
    8GP5, 8GPG, 8GPI, 8GPJ, 8GPK

  • PubMed Abstract: 

    Structure-guided immunofocusing HIV-1 vaccine design entails a comprehensive understanding of Envs from diverse HIV-1 subtypes, including circulating recombinant forms (CRFs). Here, we present the cryo-EM structures of Envs from two Asia prevalent CRFs (CRF01_AE and CRF07_BC) at 3.0 and 3.5 Å. We compare the structures and glycosylation patterns of Envs from different subtypes and perform cross-clade statistical analyses to reveal the unique features of CRF01_AE V1 region, which are associated with the resistance to certain bNAbs. We also solve a 4.1 Å cryo-EM structure of CRF01_AE Env in complex with F6, the first bNAb from CRF01_AE-infected individuals. F6 recognizes a gp120-gp41 spanning epitope to allosterically destabilize the Env trimer apex and weaken inter-protomer packing, which in turn hinders the receptor binding and induces Env trimer disassembly, demonstrating a dual mechanism of neutralization. These findings broaden our understanding of CRF Envs and shed lights on immunofocusing HIV-1 vaccine design.


  • Organizational Affiliation
    • Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.

Macromolecule Content 

  • Total Structure Weight: 124.23 kDa 
  • Atom Count: 5,470 
  • Modeled Residue Count: 646 
  • Deposited Residue Count: 1,074 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
F6 Fab VH domainA [auth E]232Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
F6 Fab VL domainB [auth F]220Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
X18 UFO Env protomerC [auth X]622Homo sapiensMutation(s): 0 
UniProt
Find proteins for A0A0E3EAY4 (Human immunodeficiency virus type 1)
Explore A0A0E3EAY4 
Go to UniProtKB:  A0A0E3EAY4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E3EAY4
Glycosylation
Glycosylation Sites: 13
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseD [auth N],
F [auth B]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth A],
G [auth C],
H [auth D],
I [auth G],
J [auth H]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-07-02
    Changes: Data collection