5BK0 | pdb_00005bk0

Crystal structure of 663 Fab bound to circumsporozoite protein NANP 5-mer

• PDB DOI: https://doi.org/10.2210/pdb5BK0/pdb

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


• Deposited: 2017-09-12 Released: 2017-12-13 
• Deposition Author(s): Scally, S.W., Bosch, A., Triller, G., Wardemann, H., Julien, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.274 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Natural Parasite Exposure Induces Protective Human Anti-Malarial Antibodies.

Triller, G., Scally, S.W., Costa, G., Pissarev, M., Kreschel, C., Bosch, A., Marois, E., Sack, B.K., Murugan, R., Salman, A.M., Janse, C.J., Khan, S.M., Kappe, S.H.I., Adegnika, A.A., Mordmuller, B., Levashina, E.A., Julien, J.P., Wardemann, H.

(2017) Immunity 47: 1197-1209.e10

• PubMed: 29195810 
• DOI: https://doi.org/10.1016/j.immuni.2017.11.007
• Primary Citation Related Structures: 
  5BK0, 5BK3, 5BK5, 6AZM, 6AZX


• PubMed Abstract: 
  

  Antibodies against the NANP repeat of circumsporozoite protein (CSP), the major surface antigen of Plasmodium falciparum (Pf) sporozoites, can protect from malaria in animal models but protective humoral immunity is difficult to induce in humans. Here we cloned and characterized rare affinity-matured human NANP-reactive memory B cell antibodies elicited by natural Pf exposure that potently inhibited parasite transmission and development in vivo. We unveiled the molecular details of antibody binding to two distinct protective epitopes within the NANP repeat. NANP repeat recognition was largely mediated by germline encoded and immunoglobulin (Ig) heavy-chain complementarity determining region 3 (HCDR3) residues, whereas affinity maturation contributed predominantly to stabilizing the antigen-binding site conformation. Combined, our findings illustrate the power of exploring human anti-CSP antibody responses to develop tools for malaria control in the mammalian and the mosquito vector and provide a molecular basis for the structure-based design of next-generation CSP malaria vaccines.

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Organizational Affiliation: 
• B Cell Immunology, German Cancer Research Center, Heidelberg, 69120, Germany.
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada.
Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, 10117, Germany.
UPR9022 CNRS, U963 Inserm, Université de Strasbourg, Strasbourg, 67000, France.
Seattle Biomedical Research Institute, Seattle, WA 98109, USA.
The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK; Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands.
Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands.
Centre de Recherches Médicales de Lambaréné, Lambaréné, 242, Gabon; Institute of Tropical Medicine and German Center for Infection Research, partner site Tübingen, University of Tübingen, Tübingen, 72074, Germany; Leiden University Medical Centre (LUMC), Leiden, 2333 ZA, The Netherlands.
Institute of Tropical Medicine and German Center for Infection Research, partner site Tübingen, University of Tübingen, Tübingen, 72074, Germany.
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; Departments of Biochemistry and Immunology, University of Toronto, ON M5G 0A4, Canada. Electronic address: [e-mail].
B Cell Immunology, German Cancer Research Center, Heidelberg, 69120, Germany. 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 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.53 kDa 
• Atom Count: 6,548 
• Modeled Residue Count: 881 
• Deposited Residue Count: 898 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
663 Antibody, light chain	A, C	217	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
663 Antibody, heavy chain	B, D	222	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Circumsporozoite protein NANP 5-mer	E	20	Plasmodium falciparum	Mutation(s): 0
UniProt
Find proteins for P02893 (Plasmodium falciparum) Explore P02893  Go to UniProtKB:  P02893

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.274 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.815	α = 90
b = 132.674	β = 93.49
c = 51.02	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-13 
Deposition Author(s): Scally, S.W., Bosch, A., Triller, G., Wardemann, H., Julien, J.P.

Revision History  

• Version 1.0: 2017-12-13
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary