8QKR | pdb_00008qkr

Plasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to R5.251

• PDB DOI: https://doi.org/10.2210/pdb8QKR/pdb

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


• Deposited: 2023-09-16 Released: 2024-07-31 
• Deposition Author(s): Wright, N.D., Barrett, J.R., Bradshaw, W.J., Paterson, N.G., MacLean, E.M., Ferreira, L., McHugh, K., Koekemoer, L., Draper, S.J.
• Funding Organization(s): University of Oxford, Medical Sciences Internal Fund (MSIF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free: 
  0.327 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

Analysis of the diverse antigenic landscape of the malaria protein RH5 identifies a potent vaccine-induced human public antibody clonotype.

Barrett, J.R., Pipini, D., Wright, N.D., Cooper, A.J.R., Gorini, G., Quinkert, D., Lias, A.M., Davies, H., Rigby, C.A., Aleshnick, M., Williams, B.G., Bradshaw, W.J., Paterson, N.G., Martinson, T., Kirtley, P., Picard, L., Wiggins, C.D., Donnellan, F.R., King, L.D.W., Wang, L.T., Popplewell, J.F., Silk, S.E., de Ruiter Swain, J., Skinner, K., Kotraiah, V., Noe, A.R., MacGill, R.S., King, C.R., Birkett, A.J., Soisson, L.A., Minassian, A.M., Lauffenburger, D.A., Miura, K., Long, C.A., Wilder, B.K., Koekemoer, L., Tan, J., Nielsen, C.M., McHugh, K., Draper, S.J.

(2024) Cell 187: 4964

• PubMed: 39059380 
• DOI: https://doi.org/10.1016/j.cell.2024.06.015
• Primary Citation of Related Structures:  
  8QKR, 8QKS


• PubMed Abstract: 
  

  The highly conserved and essential Plasmodium falciparum reticulocyte-binding protein homolog 5 (PfRH5) has emerged as the leading target for vaccines against the disease-causing blood stage of malaria. However, the features of the human vaccine-induced antibody response that confer highly potent inhibition of malaria parasite invasion into red blood cells are not well defined. Here, we characterize 236 human IgG monoclonal antibodies, derived from 15 donors, induced by the most advanced PfRH5 vaccine. We define the antigenic landscape of this molecule and establish that epitope specificity, antibody association rate, and intra-PfRH5 antibody interactions are key determinants of functional anti-parasitic potency. In addition, we identify a germline IgG gene combination that results in an exceptionally potent class of antibody and demonstrate its prophylactic potential to protect against P. falciparum parasite challenge in vivo. This comprehensive dataset provides a framework to guide rational design of next-generation vaccines and prophylactic antibodies to protect against blood-stage malaria.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK; The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK.
Centre for Medicines Discovery, University of Oxford, Oxford OX3 7FZ, UK.
Antibody Biology Unit, Laboratory of Immunogenetics, NIAID/NIH, Rockville, MD 20852, USA.
The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK.
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK.
Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK.
Department of Biological Engineering, MIT, Cambridge, MA, USA.
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK; Antibody Biology Unit, Laboratory of Immunogenetics, NIAID/NIH, Rockville, MD 20852, USA.
Carterra, 825 N. 300 W. Ste. C309, Salt Lake City, UT 84103, USA.
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK.
Leidos Life Sciences, Frederick, MD, USA.
Center for Vaccine Innovation and Access, PATH, Washington, DC 20001, USA.
USAID, 1300 Pennsylvania Avenue NW, Washington, DC 20004, USA.
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK; The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA.
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK; The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 177.22 kDa 
• Atom Count: 11,769 
• Modeled Residue Count: 1,468 
• Deposited Residue Count: 1,558 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reticulocyte-binding protein-like protein 5	A, D	325	Plasmodium falciparum	Mutation(s): 0  Gene Names: Rh5
UniProt
Find proteins for Q8IFM5 (Plasmodium falciparum (isolate 3D7)) Explore Q8IFM5  Go to UniProtKB:  Q8IFM5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
R5251VHCH	B, E	234	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
R5251VLCL	C, F	220	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free:  0.327 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.240 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.927	α = 60.535
b = 92.016	β = 72.132
c = 92.492	γ = 79.818

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Wright, N.D., Barrett, J.R., Bradshaw, W.J., Paterson, N.G., MacLean, E.M., Ferreira, L., McHugh, K., Koekemoer, L., Draper, S.J.

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Funding Organization	Location	Grant Number
University of Oxford, Medical Sciences Internal Fund (MSIF)	United Kingdom	--

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release
  
• Version 1.1: 2024-09-04
  Changes: Database references
• Version 1.2: 2024-09-18
  Changes: Database references
• Version 1.3: 2024-11-13
  Changes: Structure summary