Biological Assembly 1  

 3D View: Structure

Standalone Viewers  
Protein Workshop | Ligand Explorer

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: 318913.28 
• Atom Count: 20379 
• Residue Count: 2925 
• Unique protein chains: 4

3J5M

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

• DOI: 10.2210/pdb3J5M/pdb
• EMDataBank: EMD-5779

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1
• Expression System: Homo sapiens
• Mutation(s): 2 


• 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: 5.8 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

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

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., Lyumkis, D.

(2013) Science 342: 1484-1490

• PubMed: 24179160 
• DOI: 10.1126/science.1245627


• 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

Find similar proteins by: Sequence  |  Structure

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
BG505 SOSIP gp41	B, F, J	64	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
PGV04 light chain	C, G, K	208	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
PGV04 heavy chain	D, H, L	228	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK	B, F, J	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.8 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
  Type: Database references
• Version 1.2: 2018-07-18
  Type: Data collection