8GPG | pdb_00008gpg

HIV-1 Env X18 UFO in complex with F6 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 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: 366.8 kDa 
  • Atom Count: 15,864 
  • Modeled Residue Count: 1,920 
  • Deposited Residue Count: 3,222 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
F6 Fab heavy chain
A, C, E
232Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
F6 Fab light chain
B, D, F
220Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 Env X18 UFOG [auth X],
H [auth Y],
I [auth Z]
622Human immunodeficiency virus 1Mutation(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: 10
Sequence Annotations
Expand
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-glucopyranoseJ [auth G],
M [auth J],
P [auth M]
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-glucopyranose
K [auth H],
L [auth I],
N [auth K],
O [auth L],
Q [auth N],
K [auth H],
L [auth I],
N [auth K],
O [auth L],
Q [auth N],
R [auth O]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth Y]
BA [auth Y]
CA [auth Y]
DA [auth Y]
EA [auth Y]
AA [auth Y],
BA [auth Y],
CA [auth Y],
DA [auth Y],
EA [auth Y],
FA [auth Y],
GA [auth Z],
HA [auth Z],
IA [auth Z],
JA [auth Z],
KA [auth Z],
LA [auth Z],
MA [auth Z],
S [auth X],
T [auth X],
U [auth X],
V [auth X],
W [auth X],
X,
Y [auth X],
Z [auth Y]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2024-11-20
    Changes: Data collection, Structure summary