6B3D | pdb_00006b3d

Crystal structure of anti-HIV antibody PGT128 in complex with a bacterially derived synthetic mimetic of Man9.

• PDB DOI: https://doi.org/10.2210/pdb6B3D/pdb

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


• Deposited: 2017-09-21 Released: 2017-12-06 
• Deposition Author(s): Murrell, S., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.198 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Bacterially derived synthetic mimetics of mammalian oligomannose prime antibody responses that neutralize HIV infectivity.

Pantophlet, R., Trattnig, N., Murrell, S., Lu, N., Chau, D., Rempel, C., Wilson, I.A., Kosma, P.

(2017) Nat Commun 8: 1601-1601

• PubMed: 29150603 
• DOI: https://doi.org/10.1038/s41467-017-01640-y
• Primary Citation Related Structures: 
  6B3D


• PubMed Abstract: 
  

  Oligomannose-type glycans are among the major targets on the gp120 component of the HIV envelope protein (Env) for broadly neutralizing antibodies (bnAbs). However, attempts to elicit oligomannose-specific nAbs by immunizing with natural or synthetic oligomannose have so far not been successful, possibly due to B cell tolerance checkpoints. Here we design and synthesize oligomannose mimetics, based on the unique chemical structure of a recently identified bacterial lipooligosaccharide, to appear foreign to the immune system. One of these mimetics is bound avidly by members of a family of oligomannose-specific bnAbs and their putative common germline precursor when presented as a glycoconjugate. The crystal structure of one of the mimetics bound to a member of this bnAb family confirms the antigenic resemblance. Lastly, immunization of human-antibody transgenic animals with a lead mimetic evokes nAbs with specificities approaching those of existing bnAbs. These results provide evidence for utilizing antigenic mimicry to elicit oligomannose-specific bnAbs to HIV-1.

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Organizational Affiliation: 
• Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada, V5A1S6. [e-mail].
Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada, V5A1S6. [e-mail].
SFU Interdisciplinary Research Centre for HIV, Simon Fraser University, Burnaby, BC, Canada, V5A1S6. [e-mail].
Department of Chemistry, University of Natural Resources and Life Sciences, A-1190, Vienna, Austria.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada, V5A1S6.
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].
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 Chemistry, University of Natural Resources and Life Sciences, A-1190, Vienna, Austria. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 50.01 kDa 
• Atom Count: 3,625 
• Modeled Residue Count: 442 
• Deposited Residue Count: 450 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT128 Fab light chain	A [auth L]	211	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT128 Fab heavy chain	B [auth H]	239	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose	C [auth A]	7		N/A
Glycosylation Resources
GlyTouCan: G28309CZ GlyCosmos: G28309CZ

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	L [auth H]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	D [auth L], E [auth L], F [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth L], H [auth L], I [auth L], J [auth L], M [auth H], N [auth H]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	K [auth L], O [auth H], P [auth H]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	B [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.198 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.137	α = 90
b = 105.204	β = 90
c = 145.306	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: 2017-12-06 
Deposition Author(s): Murrell, S., Wilson, I.A.

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Polymer sequence, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary