6O29 | pdb_00006o29

Crystal structure of 4493 Fab in complex with circumsporozoite protein NPDP and anti-kappa VHH domain

• PDB DOI: https://doi.org/10.2210/pdb6O29/pdb

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


• Deposited: 2019-02-22 Released: 2020-07-01 
• Deposition Author(s): Scally, S.W., Bosch, A., Prieto, K., Murugan, R., Wardemann, H., Julien, J.P.
• Funding Organization(s): Bill & Melinda Gates Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.240 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: other

Literature

Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs.

Murugan, R., Scally, S.W., Costa, G., Mustafa, G., Thai, E., Decker, T., Bosch, A., Prieto, K., Levashina, E.A., Julien, J.P., Wardemann, H.

(2020) Nat Med 26: 1135-1145

• PubMed: 32451496 
• DOI: https://doi.org/10.1038/s41591-020-0881-9
• Primary Citation Related Structures: 
  6O23, 6O24, 6O25, 6O26, 6O28, 6O29, 6O2A, 6O2B, 6O2C, 6ULE, 6ULF, 6VLN


• PubMed Abstract: 
  

  The circumsporozoite protein of the human malaria parasite Plasmodium falciparum (PfCSP) is the main target of antibodies that prevent the infection and disease, as shown in animal models. However, the limited efficacy of the PfCSP-based vaccine RTS,S calls for a better understanding of the mechanisms driving the development of the most potent human PfCSP antibodies and identification of their target epitopes. By characterizing 200 human monoclonal PfCSP antibodies induced by sporozoite immunization, we establish that the most potent antibodies bind around a conserved (N/D)PNANPN(V/A) core. High antibody affinity to the core correlates with protection from parasitemia in mice and evolves around the recognition of NANP motifs. The data suggest that the rational design of a next-generation PfCSP vaccine that elicits high-affinity antibody responses against the core epitope will promote the induction of protective humoral immune responses.

---

Organizational Affiliation: 
• B Cell Immunology, German Cancer Research Institute (DKFZ), Heidelberg, Germany.
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.
Department of Immunology, University of Toronto, Toronto, Ontario, Canada.
Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany.
Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany. [e-mail].
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada. [e-mail].
Department of Immunology, University of Toronto, Toronto, Ontario, Canada. [e-mail].
Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. [e-mail].
B Cell Immunology, German Cancer Research Institute (DKFZ), Heidelberg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 120.67 kDa 
• Atom Count: 8,344 
• Modeled Residue Count: 1,140 
• Deposited Residue Count: 1,154 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4493 Fab heavy chain	A, C [auth H]	225	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4493 Kappa light chain	B, D [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Circumsporozoite protein	E [auth C], F [auth D]	16	Plasmodium falciparum	Mutation(s): 0
UniProt
Find proteins for P19597 (Plasmodium falciparum (isolate NF54)) Explore P19597  Go to UniProtKB:  P19597

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-kappa VHH domain	G [auth K], H [auth E]	121	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth A], J [auth B], K	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.240 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.537	α = 90
b = 79.761	β = 90
c = 281.795	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: 2020-07-01 
Deposition Author(s): Scally, S.W., Bosch, A., Prieto, K., Murugan, R., Wardemann, H., Julien, J.P.

---

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation		--

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary