7UNB | pdb_00007unb

Crystal structure of malaria transmission-blocking antigen Pfs48/45-6C variant in complex with human antibodies RUPA-117 and RUPA-47

• PDB DOI: https://doi.org/10.2210/pdb7UNB/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Plasmodium falciparum
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-04-10 Released: 2022-08-10 
• Deposition Author(s): Hailemariam, S., McLeod, B., Julien, J.-P.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation, Canadian Institutes of Health Research (CIHR), CIFAR Azrieli Global Scholars, Ontario Early Researcher Awards, Canada Research Chairs

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Vaccination with a structure-based stabilized version of malarial antigen Pfs48/45 elicits ultra-potent transmission-blocking antibody responses.

McLeod, B., Mabrouk, M.T., Miura, K., Ravichandran, R., Kephart, S., Hailemariam, S., Pham, T.P., Semesi, A., Kucharska, I., Kundu, P., Huang, W.C., Johnson, M., Blackstone, A., Pettie, D., Murphy, M., Kraft, J.C., Leaf, E.M., Jiao, Y., van de Vegte-Bolmer, M., van Gemert, G.J., Ramjith, J., King, C.R., MacGill, R.S., Wu, Y., Lee, K.K., Jore, M.M., King, N.P., Lovell, J.F., Julien, J.P.

(2022) Immunity 55: 1680-1692.e8

• PubMed: 35977542 
• DOI: https://doi.org/10.1016/j.immuni.2022.07.015
• Primary Citation Related Structures: 
  7UNB


• PubMed Abstract: 
  

  Malaria transmission-blocking vaccines (TBVs) aim to elicit human antibodies that inhibit sporogonic development of Plasmodium falciparum in mosquitoes, thereby preventing onward transmission. Pfs48/45 is a leading clinical TBV candidate antigen and is recognized by the most potent transmission-blocking monoclonal antibody (mAb) yet described; still, clinical development of Pfs48/45 antigens has been hindered, largely by its poor biochemical characteristics. Here, we used structure-based computational approaches to design Pfs48/45 antigens stabilized in the conformation recognized by the most potently inhibitory mAb, achieving >25°C higher thermostability compared with the wild-type protein. Antibodies elicited in mice immunized with these engineered antigens displayed on liposome-based or protein nanoparticle-based vaccine platforms exhibited 1-2 orders of magnitude superior transmission-reducing activity, compared with immunogens bearing the wild-type antigen, driven by improved antibody quality. Our data provide the founding principles for using molecular stabilization solely from antibody structure-function information to drive improved immune responses against a parasitic vaccine target.

---

Organizational Affiliation: 
• Program in Molecular Medicine, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA.
Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12735 Twinbrook Parkway, Rockville, MD 20852, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA.
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, ON M5G 0A4, Canada.
Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands.
Radboud Institute for Health Sciences, Department for Health Evidence, Biostatistics Section, Radboud University Medical Center, Nijmegen, the Netherlands.
PATH's Malaria Vaccine Initiative, 455 Massachusetts Avenue NW Suite 1000, Washington, DC 20001, USA.
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 111.73 kDa 
• Atom Count: 8,338 
• Modeled Residue Count: 1,017 
• Deposited Residue Count: 1,029 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RUPA-47 Fab kappa chain	A [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gametocyte surface protein P45/48	B [auth R]	147	Plasmodium falciparum	Mutation(s): 3  Gene Names: PF45/48, PFS45-48, PFS45/48, PF13_0247, PF3D7_1346700
UniProt
Find proteins for Q8I6T1 (Plasmodium falciparum (isolate 3D7)) Explore Q8I6T1  Go to UniProtKB:  Q8I6T1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RUPA-117 Fab kappa chain	C [auth E]	214	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RUPA-47 Fab heavy chain	D [auth H]	223	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RUPA-117 Fab heavy chain	E [auth F]	230	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	F	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.669	α = 90
b = 127.16	β = 90
c = 132.706	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Hailemariam, S., McLeod, B., Julien, J.-P.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R01AI148557-01A1
Bill & Melinda Gates Foundation	United States	OPP1156262
Canadian Institutes of Health Research (CIHR)	Canada	428410
Bill & Melinda Gates Foundation	United States	OPP1179906
CIFAR Azrieli Global Scholars	Canada	--
Ontario Early Researcher Awards	Canada	--
Canada Research Chairs	Canada	--

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2022-08-31
  Changes: Database references
• Version 1.2: 2022-09-28
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary