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- PDB-9zrj: cryoEM structure of hexametric HtrA from Borrelia burgdorferi wit... -

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Basic information

Entry
Database: PDB / ID: 9zrj
TitlecryoEM structure of hexametric HtrA from Borrelia burgdorferi with bound peptides in the active sites
Components
  • Periplasmic serine protease DO
  • UNKNOWN fragment
KeywordsHYDROLASE / serine protease / chaperone / PDZ domain / protein maturation / protein degradation
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase S1C, Do / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Periplasmic serine protease DO
Similarity search - Component
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
unidentified (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShakya, A.K. / Herzberg, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI080615 United States
CitationJournal: J Mol Biol / Year: 2026
Title: Assembly and Flexibility of Borrelia burgdorferi Periplasmic HtrA Hexamers.
Authors: Anil Kumar Shakya / D Travis Gallager / Vipin Singh Rana / Suruchi Singh / S Saif Hasan / Utpal Pal / Osnat Herzberg /
Abstract: The chaperone/protease HtrA from the Lyme disease pathogen Borrelia burgdorferi (BbHtrA) functions in the maturation of the periplasmic protein BB0323 involved in pathogen infectivity and in the ...The chaperone/protease HtrA from the Lyme disease pathogen Borrelia burgdorferi (BbHtrA) functions in the maturation of the periplasmic protein BB0323 involved in pathogen infectivity and in the degradation of several other key host and spirochete proteins. Hence, BbHtrA is considered an anti-borrelial drug target candidate. BbHtrA contains a N-terminal serine protease domain followed by two PDZ domains (PDZ1-2). Here, we report a 3.4 Å resolution single particle cryo-EM reconstruction of hexameric BbHtrA whose active site serine was replaced by an alanine, and the 2.0 Å and 1.5 Å resolution crystal structures of the recombinant protease catalytic domain and PDZ1-2 fragment, respectively. The BbHtrA cryo-EM structure forms an asymmetric dimer of trimers unlike the symmetric oligomers of other HtrA family members. The different conformations of the six linkers between the protease domains and their respective PDZ1-2 break the symmetry, nevertheless, pairs of PDZ2 domains mediate trimer-trimer interactions through identical interfaces unique to BbHtrA. Features associated with the cryo-EM electron potential map at each protease active site were modeled as a nine-residue peptide of unknown sequence, which could originate from the expression host organism. The crystal structures recapitulate at higher resolution trimer interactions via the catalytic domains and trimer-trimer association via PDZ2-PDZ2 interactions. The serine protease oxyanion hole that stabilizes the substrate transition state is malformed in the crystal structure and fully formed in the peptide-bound BbHtrA cryo-EM structure, suggesting a regulatory mechanism intended to avoid undesired cleavage.
History
DepositionDec 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic serine protease DO
B: Periplasmic serine protease DO
C: Periplasmic serine protease DO
D: Periplasmic serine protease DO
E: Periplasmic serine protease DO
F: Periplasmic serine protease DO
G: UNKNOWN fragment
H: UNKNOWN fragment
I: UNKNOWN fragment
J: UNKNOWN fragment
K: UNKNOWN fragment
L: UNKNOWN fragment


Theoretical massNumber of molelcules
Total (without water)300,67912
Polymers300,67912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Periplasmic serine protease DO


Mass: 49329.227 Da / Num. of mol.: 6 / Mutation: S226A
Source method: isolated from a genetically manipulated source
Details: 28 N-terminal signal sequence is omitted from the expression construct. Precession protease cleavage and BamH1 site adds GPLGS at the N-terminus.
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Strain: ATCC 35210 / Gene: BB_0104 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(D3) / References: UniProt: O51131
#2: Protein/peptide
UNKNOWN fragment


Mass: 783.958 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: 9 amino acids of unknown sequence modeled as alanine residues
Source: (natural) unidentified (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Borrelia burgdorferi HtrA with a bound peptide of unknown sequence
Type: COMPLEX
Details: Hexamer complex of HtrA with an unknown peptide bound in the active site of each monomer and modeled as nine alanine residues.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: YES
Source (natural)Organism: Borreliella burgdorferi (Lyme disease spirochete) / Strain: ATCC 35210
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtris(hydroxymethyl)aminomethane hydrochlorideTris-HCL1
2200 mMSodium chlorideNaCl1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: OTHER

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.4.1particle selection
4cryoSPARCv4.4.1CTF correction
7Coot9.03model fitting
9PHENIX1.21model refinement
13cryoSPARCv4.4.13D reconstruction
Image processingDetails: k3
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157066 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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