Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 50114.64 
• Atom Count: 3473 
• Residue Count: 450 
• Unique protein chains: 2

6B3D

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

• DOI: 10.2210/pdb6B3D/pdb

• Classification: IMMUNE SYSTEM
• Expression System: Homo sapiens


• 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: 2.271 Å
• R-Value Free: 0.198 
• R-Value Work: 0.163 

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: 10.1038/s41467-017-01640-y


• 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].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PGT128 Fab light chain	L	211	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PGT128 Fab heavy chain	H	239	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EPE	H	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HEPES C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	L	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAN	H	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
EDO	H, L	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	H, L	ISOPROPYL ALCOHOL 2-PROPANOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	H	L-PEPTIDE LINKING	C5 H7 N O3		GLU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.271 Å
• R-Value Free: 0.198 
• R-Value Work: 0.163 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 72.137	α = 90.00
b = 105.204	β = 90.00
c = 145.306	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History 

• Version 1.0: 2017-12-06
  Type: Initial release