6AVN | pdb_00006avn

Crystal structure of unbound anti-HIV antibody Fab PGV19 at 2.5 A

• PDB DOI: https://doi.org/10.2210/pdb6AVN/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-09-03 Released: 2018-06-27 
• Deposition Author(s): Sarkar, A., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer.

Sarkar, A., Bale, S., Behrens, A.J., Kumar, S., Sharma, S.K., de Val, N., Pallesen, J., Irimia, A., Diwanji, D.C., Stanfield, R.L., Ward, A.B., Crispin, M., Wyatt, R.T., Wilson, I.A.

(2018) Nat Commun 9: 1956-1956

• PubMed: 29769533 
• DOI: https://doi.org/10.1038/s41467-018-04272-y
• Primary Citation Related Structures: 
  6AVN, 6B0N


• PubMed Abstract: 
  

  Furin cleavage of the HIV envelope glycoprotein is an essential step for cell entry that enables formation of well-folded, native-like glycosylated trimers, releases constraints on the fusion peptide, and limits enzymatic processing of the N-glycan shield. Here, we show that a cleavage-independent, stabilized, soluble Env trimer mimic (BG505 NFL.664) exhibits a "closed-form", native-like, prefusion conformation akin to furin-cleaved Env trimers. The crystal structure of BG505 NFL.664 at 3.39 Å resolution with two potent bNAbs also identifies the full epitopes of PGV19 and PGT122 that target the receptor binding site and N332 supersite, respectively. Quantitative site-specific analysis of the glycan shield reveals that native-like glycan processing is maintained despite furin-independent maturation in the secretory pathway. Thus, cleavage-independent NFL Env trimers exhibit quaternary protein and carbohydrate structures similar to the native viral spike that further validate their potential as vaccine immunogen candidates.

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Organizational Affiliation: 
• IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA. [e-mail].
Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA. [e-mail].
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA. [e-mail].
IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA. [e-mail].
Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA. [e-mail].
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. [e-mail].
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.07 kDa 
• Atom Count: 3,414 
• Modeled Residue Count: 426 
• Deposited Residue Count: 432 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PGV19 Fab heavy chain	A [auth H]	223	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PGV19 Fab light chain	B [auth L]	209	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	E [auth H]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
GOL	C [auth H], D [auth H], F [auth L], G [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.783	α = 90
b = 69.783	β = 90
c = 193.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): Sarkar, A., Wilson, I.A.

Revision History  

• Version 1.0: 2018-06-27
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary