Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 21-mer - A3BCDEFG Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 21-mer - A6BC3DE 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 614.61 kDa 
• Atom Count: 41285 
• Residue Count: 5066 
• Unique protein chains: 7

5WDU

HIV-1 Env BG505 SOSIP.664 H72C-H564C trimer in complex with bNAbs PGT122 Fab, 35O22 Fab and NIH45-46 scFv

• DOI: 10.2210/pdb5WDU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-07-06 Released: 2018-04-04 
• Deposition Author(s): Julien, J.-P., Torrents de la Pena, A., Sanders, R.W., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), International AIDS Vaccine Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 7.00 Å
• R-Value Free: 0.363 
• R-Value Work: 0.301 
• R-Value Observed: 0.304 

Literature

Improving the Immunogenicity of Native-like HIV-1 Envelope Trimers by Hyperstabilization.

Torrents de la Pena, A., Julien, J.P., de Taeye, S.W., Garces, F., Guttman, M., Ozorowski, G., Pritchard, L.K., Behrens, A.J., Go, E.P., Burger, J.A., Schermer, E.E., Sliepen, K., Ketas, T.J., Pugach, P., Yasmeen, A., Cottrell, C.A., Torres, J.L., Vavourakis, C.D., van Gils, M.J., LaBranche, C., Montefiori, D.C., Desaire, H., Crispin, M., Klasse, P.J., Lee, K.K., Moore, J.P., Ward, A.B., Wilson, I.A., Sanders, R.W.

(2017) Cell Rep 20: 1805-1817

• PubMed: 28834745 
• DOI: 10.1016/j.celrep.2017.07.077
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The production of native-like recombinant versions of the HIV-1 envelope glycoprotein (Env) trimer requires overcoming the natural flexibility and instability of the complex. The engineered BG505 SOSIP.664 trimer mimics the structure and antigenicity of native Env. Here, we describe how the introduction of new disulfide bonds between the glycoprotein (gp)120 and gp41 subunits of SOSIP trimers of the BG505 and other genotypes improves their stability and antigenicity, reduces their conformational flexibility, and helps maintain them in the unliganded conformation. The resulting next-generation SOSIP.v5 trimers induce strong autologous tier-2 neutralizing antibody (NAb) responses in rabbits. In addition, the BG505 SOSIP.v6 trimers induced weak heterologous NAb responses against a subset of tier-2 viruses that were not elicited by the prototype BG505 SOSIP.664. These stabilization methods can be applied to trimers from multiple genotypes as components of multivalent vaccines aimed at inducing broadly NAbs (bNAbs).

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Organizational Affiliation: 

Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein gp160	F, G, Q	471	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
bnAb NIH45-46 scFv	D, O, W	250	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein gp160	A, J, R	147	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Go to UniProtKB:  Q2N0S6

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
bnAb PGT122 Fab light chain	B, K, S	210	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
bnAb PGT122 Fab heavy chain	C, L, T	232	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
bnAb 35O55 Fab heavy chain	H, M, U	242	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
bnAb 35O22 Fab light chain	I, N, V	213	Homo sapiens	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
NAG	A, F, G, J, Q, R	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA	F, G, Q	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	F, G, Q	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	D,O,W	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 7.00 Å
• R-Value Free: 0.363 
• R-Value Work: 0.301 
• R-Value Observed: 0.304 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 361.81	α = 90
b = 215.85	β = 114.03
c = 176.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-07-06 
• Released Date: 2018-04-04 
Deposition Author(s): Julien, J.-P., Torrents de la Pena, A., Sanders, R.W., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI110657
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Scripps CHAVI-ID UM1 AI100663
International AIDS Vaccine Initiative	United States	IAVI

Revision History 

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2019-12-11
  Changes: Author supporting evidence, Polymer sequence
• Version 3.0: 2020-01-01
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary