Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 18-mer - A3B3C3D3E3F3 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 18-mer -A6B6C3D3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 176766.95 
• Atom Count: 11728 
• Residue Count: 1537 
• Unique protein chains: 6

5W6D

Crystal structure of BG505-SOSIP.v4.1-GT1-N137A in complex with Fabs 35022 and 9H/109L

• DOI: 10.2210/pdb5W6D/pdb

• Classification: VIRAL PROTEIN/Immune System
• Organism(s): Human immunodeficiency virus 1
• Expression System: Homo sapiens


• Deposited: 2017-06-16 Released: 2017-07-05 
• Deposition Author(s): Garces, F., Stanfield, R.L., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.202 Å
• R-Value Free: 0.267 
• R-Value Work: 0.242 

Literature

Design and crystal structure of a native-like HIV-1 envelope trimer that engages multiple broadly neutralizing antibody precursors in vivo.

Medina-Ramirez, M., Garces, F., Escolano, A., Skog, P., de Taeye, S.W., Del Moral-Sanchez, I., McGuire, A.T., Yasmeen, A., Behrens, A.J., Ozorowski, G., van den Kerkhof, T.L.G.M., Freund, N.T., Dosenovic, P., Hua, Y., Gitlin, A.D., Cupo, A., van der Woude, P., Golabek, M., Sliepen, K., Blane, T., Kootstra, N., van Breemen, M.J., Pritchard, L.K., Stanfield, R.L., Crispin, M., Ward, A.B., Stamatatos, L., Klasse, P.J., Moore, J.P., Nemazee, D., Nussenzweig, M.C., Wilson, I.A., Sanders, R.W.

(2017) J. Exp. Med. 214: 2573-2590

• PubMed: 28847869 
• DOI: 10.1084/jem.20161160


• PubMed Abstract: 
  

Induction of broadly neutralizing antibodies (bNAbs) by HIV-1 envelope glycoprotein immunogens would be a major advance toward an effective vaccine. A critical step in this process is the activation of naive B cells expressing germline (gl) antibody precursors that have the potential to evolve into bNAbs. Here, we reengineered the BG505 SOSIP.664 glycoprotein to engage gl precursors of bNAbs that target either the trimer apex or the CD4-binding site. The resulting BG505 SOSIP.v4.1-GT1 trimer binds multiple bNAb gl precursors in vitro. Immunization experiments in knock-in mice expressing gl-VRC01 or gl-PGT121 show that this trimer activates B cells in vivo, resulting in the secretion of specific antibodies into the sera. A crystal structure of the gl-targeting trimer at 3.2-Å resolution in complex with neutralizing antibodies 35O22 and 9H+109L reveals a native-like conformation and the successful incorporation of design features associated with binding of multiple gl-bNAb precursors.

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Organizational Affiliation: 

Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
BG505-SOSIP.v4.1-GT1-N137A gp120	G	474	Human immunodeficiency virus 1	Mutation(s): 0  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.v4.1-GT1-N137A gp41	B	153	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Go to UniProtKB:  Q2N0S6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
109L FAB light chain	L	218	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
9H FAB heavy chain	H	236	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
35022 FAB heavy chain	D	240	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
35022 FAB light chain	E	216	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MAN	G	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	G	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	B, G	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.202 Å
• R-Value Free: 0.267 
• R-Value Work: 0.242 
• Space Group: P 6₃

Unit Cell:

Length (Å)	Angle (°)
a = 126.952	α = 90.00
b = 126.952	β = 90.00
c = 315.199	γ = 120.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-06-16 
• Released Date: 2017-07-05 
• Deposition Author(s): Garces, F., Stanfield, R.L., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases	United States	AI110657

Revision History 

• Version 1.0: 2017-07-05
  Type: Initial release
• Version 1.1: 2017-09-13
  Type: Database references
• Version 1.2: 2017-09-27
  Type: Author supporting evidence