Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 318.91 kDa 
• Atom Count: 20379 
• Modelled Residue Count: 2733 
• Deposited Residue Count: 2925 
• Unique protein chains: 4

3J5M

Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs

• PDB DOI: 10.2210/pdb3J5M/pdb
• EM Map EMD-5779:EMDBEMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2013-10-26 Released: 2013-11-13 
• Deposition Author(s): Lyumkis, D., Julien, J.-P., Wilson, I.A., Ward, A.B.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer.

Lyumkis, D., Julien, J.P., de Val, N., Cupo, A., Potter, C.S., Klasse, P.J., Burton, D.R., Sanders, R.W., Moore, J.P., Carragher, B., Wilson, I.A., Ward, A.B.

(2013) Science 342: 1484-1490

• PubMed: 24179160 
• DOI: 10.1126/science.1245627
• Primary Citation of Related Structures:  
  3J5M


• PubMed Abstract: 
  

The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly neutralizing antibodies (bnAbs), Env is a focus for rational vaccine design. We present a cryo-electron microscopy reconstruction and structural model of a cleaved, soluble Env trimer (termed BG505 SOSIP.664 gp140) in complex with a CD4 binding site (CD4bs) bnAb, PGV04, at 5.8 angstrom resolution. The structure reveals the spatial arrangement of Env components, including the V1/V2, V3, HR1, and HR2 domains, as well as shielding glycans. The structure also provides insights into trimer assembly, gp120-gp41 interactions, and the CD4bs epitope cluster for bnAbs, which covers a more extensive area and defines a more complex site of vulnerability than previously described.

---

Organizational Affiliation: 

National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 SOSIP gp120	A, E, I	475	Human immunodeficiency virus 1	Mutation(s): 2  Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 SOSIP gp41	B, F, J	64	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PGV04 light chain	C, G, K	208	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PGV04 heavy chain	D, H, L	228	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-26 
• Released Date: 2013-11-13 
Deposition Author(s): Lyumkis, D., Julien, J.-P., Wilson, I.A., Ward, A.B.

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release
  
• Version 1.1: 2014-01-08
  Changes: Database references
• Version 1.2: 2018-07-18
  Changes: Data collection