9CCA | pdb_00009cca

Cryo-EM structure of a designed pyridoxal phosphate (PLP) synthase fused to a designed circumsporozoite protein antigen from Plasmodium falciparum (CSP-P1-CSP and CSP-P2-CSP)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A Plasmodium-derived nanoparticle vaccine elicits sterile protection against malaria in mice.

Shi, D.Ma, R.Gupta, R.Dickey, T.H.Patel, P.N.Salinas, N.D.Tang, W.K.Queen, A.Singleton, M.Delbe, N.Conteh, S.Lambert, L.E.Duffy, P.E.Tolia, N.H.

(2025) Nat Microbiol 

  • DOI: https://doi.org/10.1038/s41564-025-02209-y
  • Primary Citation of Related Structures:  
    9CCA

  • PubMed Abstract: 

    Protein nanoparticles in infectious disease vaccines enable protection through the periodic arrangement of antigens on their surface. These nanoparticles arise from organisms unrelated to the target disease, limiting their role as presentation platforms. Nanoparticles may also be compromised by pre-existing immunity to the nanoparticle carrier and may induce autoimmunity if conserved epitopes exist. Here we developed a potent multivalent malaria vaccine using an engineered Plasmodium falciparum pyridoxal 5'-phosphate (PLP) synthase as a nanoparticle that presents a designed P. falciparum circumsporozoite protein (CSP) and the Plasmodium vivax cell-transversal protein for ookinetes and sporozoites (CelTOS). These engineered vaccines elicited high titres of anti-CSP and anti-CelTOS antibodies, and three doses provided complete sterile protection against malaria in a mouse model. Cryogenic electron microscopy resolved a 2.95-Å resolution structure of the PLP nanoparticle including amino acid changes engineered to stabilize the nanoparticle. PLP synthase has no identifiable human ortholog limiting its propensity for autoimmunity or pre-existing immunity, and the engineered nanoparticles possess desirable manufacturing characteristics. These studies established an effective nanoparticle platform for malaria and infectious disease vaccines.


  • Organizational Affiliation
    • Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1
A, B, C, D, E
A, B, C, D, E, F, M, N, O, P, Q, R
537Plasmodium falciparumMutation(s): 3 
Gene Names: CSPPF3D7_0304600pdx1PFF1025c
EC: 4.3.3.6
UniProt
Find proteins for Q7K740 (Plasmodium falciparum (isolate 3D7))
Explore Q7K740 
Go to UniProtKB:  Q7K740
Find proteins for C6KT50 (Plasmodium falciparum (isolate 3D7))
Explore C6KT50 
Go to UniProtKB:  C6KT50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ7K740C6KT50
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit PDX2
G, H, I, J, K
G, H, I, J, K, L, S, T, U, V, W, X
454Plasmodium falciparumMutation(s): 3 
Gene Names: CSPPF3D7_0304600PDX2PF11_0169PF3D7_1116200
EC: 4.3.3.6 (PDB Primary Data), 3.5.1.2 (PDB Primary Data)
UniProt
Find proteins for Q7K740 (Plasmodium falciparum (isolate 3D7))
Explore Q7K740 
Go to UniProtKB:  Q7K740
Find proteins for Q8IIK4 (Plasmodium falciparum (isolate 3D7))
Explore Q8IIK4 
Go to UniProtKB:  Q8IIK4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ7K740Q8IIK4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1ZIAAI001253

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-31
    Type: Initial release