6PHG | pdb_00006phg

Predicted germline variant of human transmission blocking antibody 2544

• PDB DOI: https://doi.org/10.2210/pdb6PHG/pdb

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


• Deposited: 2019-06-25 Released: 2019-10-02 
• Deposition Author(s): McLeod, B.R., Julien, J.P.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.228 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: other

Literature

Potent antibody lineage against malaria transmission elicited by human vaccination with Pfs25.

McLeod, B., Miura, K., Scally, S.W., Bosch, A., Nguyen, N., Shin, H., Kim, D., Volkmuth, W., Ramisch, S., Chichester, J.A., Streatfield, S., Woods, C., Schief, W.R., Emerling, D., King, C.R., Julien, J.P.

(2019) Nat Commun 10: 4328-4328

• PubMed: 31551421 
• DOI: https://doi.org/10.1038/s41467-019-11980-6
• Primary Citation Related Structures: 
  6PHB, 6PHC, 6PHD, 6PHF, 6PHG, 6PHH


• PubMed Abstract: 
  

  Transmission-blocking vaccines have the potential to be key contributors to malaria elimination. Such vaccines elicit antibodies that inhibit parasites during their development in Anopheles mosquitoes, thus breaking the cycle of transmission. To date, characterization of humoral responses to Plasmodium falciparum transmission-blocking vaccine candidate Pfs25 has largely been conducted in pre-clinical models. Here, we present molecular analyses of human antibody responses generated in a clinical trial evaluating Pfs25 vaccination. From a collection of monoclonal antibodies with transmission-blocking activity, we identify the most potent transmission-blocking antibody yet described against Pfs25; 2544. The interactions of 2544 and three other antibodies with Pfs25 are analyzed by crystallography to understand structural requirements for elicitation of human transmission-blocking responses. Our analyses provide insights into Pfs25 immunogenicity and epitope potency, and detail an affinity maturation pathway for a potent transmission-blocking antibody in humans. Our findings can be employed to guide the design of improved malaria transmission-blocking vaccines.

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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.
Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12735 Twinbrook Parkway, Rockville, MD, 20852, USA.
Atreca, 500 Saginaw Drive, Redwood City, CA, 94063-4750, USA.
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Gene Therapy Program & Orphan Disease Center, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, 19104, USA.
Fraunhofer USA Center for Molecular Biotechnology CMB, 9 Innovation Way, Newark, DE, 19711, USA.
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. [e-mail].
Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada. [e-mail].
Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada. [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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.42 kDa 
• Atom Count: 3,434 
• Modeled Residue Count: 427 
• Deposited Residue Count: 446 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Germline 2544 Antibody Fab, Heavy Chain	A	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Germline 2544 Antibody Fab, Light Chain	B	218	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.228 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.843	α = 90
b = 60.557	β = 113.62
c = 61.079	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-02 
Deposition Author(s): McLeod, B.R., Julien, J.P.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	Canada	OPP1108403

Revision History  

• Version 1.0: 2019-10-02
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary