9F1V | pdb_00009f1v

Crystal structure of Borrelia burgdorferi CspZ-YA

• PDB DOI: https://doi.org/10.2210/pdb9F1V/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Borreliella burgdorferi B31
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-04-20 Released: 2025-04-16 
• Deposition Author(s): Brangulis, K., Malfetano, J., Marcinkiewicz, A.L., Wang, A., Chen, Y.-L., Yang, X., Lee, W., Bottazzi, M.-E., Pal, U., Hsieh, C.-L., Chen, W.-H., Lin, Y.-P.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Mechanistic insights into the structure-based design of a CspZ-targeting Lyme disease vaccine.

Brangulis, K., Malfetano, J., Marcinkiewicz, A.L., Wang, A., Chen, Y.L., Lee, J., Liu, Z., Yang, X., Strych, U., Tupina, D., Akopjana, I., Bottazzi, M.E., Pal, U., Hsieh, C.L., Chen, W.H., Lin, Y.P.

(2025) Nat Commun 16: 2898-2898

• PubMed: 40189575 
• DOI: https://doi.org/10.1038/s41467-025-58182-x
• Primary Citation of Related Structures:  
  9F1V, 9F21


• PubMed Abstract: 
  

  Borrelia burgdorferi (Bb) causes Lyme disease (LD), one of the most common vector-borne diseases in the Northern Hemisphere. Here, we solve the crystal structure of a mutated Bb vaccine antigen, CspZ-YA that lacks the ability to bind to host complement factor H (FH). We generate point mutants of CspZ-YA and identify CspZ-YA _I183Y and CspZ-YA _C187S to trigger more robust bactericidal responses. Compared to CspZ-YA, these CspZ-YA mutants require a lower immunization frequency to protect mice from LD-associated inflammation and bacterial colonization. Antigenicity of wild-type and mutant CspZ-YA proteins are similar, as measured using sera from infected people or immunized female mice. Structural comparison of CspZ-YA with CspZ-YA _I183Y and CspZ-YA _C187S shows enhanced interactions of two helices adjacent to the FH-binding sites in the mutants, consistent with their elevated thermostability. In line with these findings, protective CspZ-YA monoclonal antibodies show increased binding to CspZ-YA at a physiological temperature (37 °C). In summary, this proof-of-concept study applies structural vaccinology to enhance intramolecular interactions for the long-term stability of a Bb antigen while maintaining its protective epitopes, thus promoting LD vaccine development.

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Organizational Affiliation: 
• Latvian Biomedical Research and Study Centre, Riga, Latvia. [e-mail].
Department of Human Physiology and Biochemistry, Riga Stradins University, Riga, Latvia. [e-mail].
Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA.
Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA.
Pomona College, Claremont, CA, USA.
Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA.
Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA.
Department of Veterinary Medicine, Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD, USA.
Latvian Biomedical Research and Study Centre, Riga, Latvia.
Department of Biology, Baylor University, Waco, TX, USA.
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA. [e-mail].
Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA. [e-mail].
Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA. [e-mail].
Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA. [e-mail].
Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA. [e-mail].
Department of Biomedical Sciences, SUNY Albany, Albany, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.17 kDa 
• Atom Count: 1,941 
• Modeled Residue Count: 217 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement regulator-acquiring surface protein 2 (CRASP-2)	A	221	Borreliella burgdorferi B31	Mutation(s): 2  Gene Names: cspZ, BB_H06
UniProt
Find proteins for O50665 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)) Explore O50665  Go to UniProtKB:  O50665

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.469	α = 90
b = 41.552	β = 90
c = 162.564	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Brangulis, K., Malfetano, J., Marcinkiewicz, A.L., Wang, A., Chen, Y.-L., Yang, X., Lee, W., Bottazzi, M.-E., Pal, U., Hsieh, C.-L., Chen, W.-H., Lin, Y.-P.

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Funding Organization	Location	Grant Number
Other government		lzp-2021/1-0068

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release