9C79 | pdb_00009c79

Human monoclonal antibody MAD21-101 bound to the N-terminus of cleaved circumsporozoite protein

PDB DOI: https://doi.org/10.2210/pdb9C79/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Plasmodium falciparum 3D7
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2024-06-10 Released: 2024-12-25
Deposition Author(s): Moskovitz, R., Wilson, I.A.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Protective antibodies target cryptic epitope unmasked by cleavage of malaria sporozoite protein.

Dacon, C., Moskovitz, R., Swearingen, K., Da Silva Pereira, L., Flores-Garcia, Y., Aleshnick, M., Kanatani, S., Flynn, B., Molina-Cruz, A., Wollenberg, K., Traver, M., Kirtley, P., Purser, L., Dillon, M., Bonilla, B., Franco, A., Petros, S., Kritzberg, J., Tucker, C., Paez, G.G., Gupta, P., Shears, M.J., Pazzi, J., Edgar, J.M., Teng, A.A., Belmonte, A., Oda, K., Doumbo, S., Krymskaya, L., Skinner, J., Li, S., Ghosal, S., Kayentao, K., Ongoiba, A., Vaughan, A., Campo, J.J., Traore, B., Barillas-Mury, C., Wijayalath, W., Idris, A., Crompton, P.D., Sinnis, P., Wilder, B.K., Zavala, F., Seder, R.A., Wilson, I.A., Tan, J.

(2025) Science 387: eadr0510-eadr0510

PubMed: 39745947 Search on PubMed
DOI: https://doi.org/10.1126/science.adr0510
Primary Citation of Related Structures:
9C79, 9C7D, 9C7F

PubMed Abstract:
The most advanced monoclonal antibodies (mAbs) and vaccines against malaria target the central repeat region or closely related sequences within the Plasmodium falciparum circumsporozoite protein (PfCSP). Here, using an antigen-agnostic strategy to investigate human antibody responses to whole sporozoites, we identified a class of mAbs that target a cryptic PfCSP epitope that is only exposed after cleavage and subsequent pyroglutamylation (pGlu) of the newly formed N terminus. This pGlu-CSP epitope is not targeted by current anti-PfCSP mAbs and is not included in the licensed malaria vaccines. MAD21-101, the most potent mAb in this class, confers sterile protection against Pf infection in a human liver-chimeric mouse model. These findings reveal a site of vulnerability on the sporozoite surface that can be targeted by next-generation antimalarial interventions.

Organizational Affiliation

Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.

Institute for Systems Biology, Seattle, WA, USA.

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

Department of Molecular Microbiology and Immunology and Johns Hopkins Malaria Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.

Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, OR, USA.

Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.

Bioinformatics & Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.

Department of Biology, The Catholic University of America, Washington, DC, USA.

Seattle Children's Research Institute, Seattle, WA, USA.

Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.

Antigen Discovery, Incorporated, Irvine, CA, USA.

General Dynamics Information Technology, Inc., Falls Church, VA, USA.

Agile Vaccines and Therapeutics Department, Naval Medical Research Command, Silver Spring, MD, USA.

Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.

Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali.

Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.

The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.

The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.

Macromolecule Content

Total Structure Weight: 50.88 kDa
Atom Count: 4,113
Modeled Residue Count: 462
Deposited Residue Count: 464
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal antibody MAD21-101 Fab Heavy Chain	A [auth H]	228	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal antibody MAD21-101 Fab Light Chain	B [auth L]	218	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Circumsporozoite protein	C [auth D]	18	Plasmodium falciparum 3D7	Mutation(s): 0
UniProt
Find proteins for Q7K740 (Plasmodium falciparum (isolate 3D7)) Explore Q7K740 Go to UniProtKB: Q7K740
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7K740
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	2		N/A	Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain L MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain L mmCIF format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth L] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain L	E [auth H] F [auth H] G [auth H] H I [auth L] E [auth H], F [auth H], G [auth H], H, I [auth L], J [auth L], K [auth L], L	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1LUV Query on A1LUV	A [auth H]	L-PEPTIDE LINKING	C₆ H₁₅ N₂ O₃		LYS
PCA Query on PCA	C [auth D]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN