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- EMDB-74618: cryoEM structure of hexametric HtrA from Borrelia burgdorferi wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-74618
TitlecryoEM structure of hexametric HtrA from Borrelia burgdorferi with bound peptides in the active sites
Map data
Sample
  • Complex: Borrelia burgdorferi HtrA with a bound peptide of unknown sequence
    • Protein or peptide: Periplasmic serine protease DO
    • Protein or peptide: UNKNOWN fragment
Keywordsserine protease / chaperone / PDZ domain / protein maturation / protein degradation / HYDROLASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShakya AK / Herzberg O
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74618.png

Downloads & links

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Map

FileDownload / File: emd_74618.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.6316272 - 1.1035883
Average (Standard dev.)-0.0005854477 (±0.021338118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 309.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_74618_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74618_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Borrelia burgdorferi HtrA with a bound peptide of unknown sequence

EntireName: Borrelia burgdorferi HtrA with a bound peptide of unknown sequence
Components
  • Complex: Borrelia burgdorferi HtrA with a bound peptide of unknown sequence
    • Protein or peptide: Periplasmic serine protease DO
    • Protein or peptide: UNKNOWN fragment

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Supramolecule #1: Borrelia burgdorferi HtrA with a bound peptide of unknown sequence

SupramoleculeName: Borrelia burgdorferi HtrA with a bound peptide of unknown sequence
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Hexamer complex of HtrA with an unknown peptide bound in the active site of each monomer and modeled as nine alanine residues.
Source (natural)Organism: Borreliella burgdorferi (Lyme disease spirochete) / Strain: ATCC 35210
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Periplasmic serine protease DO

MacromoleculeName: Periplasmic serine protease DO / type: protein_or_peptide / ID: 1
Details: 28 N-terminal signal sequence is omitted from the expression construct. Precession protease cleavage and BamH1 site adds GPLGS at the N-terminus.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi (Lyme disease spirochete) / Strain: ATCC 35210
Molecular weightTheoretical: 49.329227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSSNRSN IVFAEEKDNT VRALQDSFRE VSKKILPSSV EVHATGVIKQ SFPIPFFFFD MPEFDSERKS NWAGSGVIIG RDSQKKSLF YVVTNSHVVD KATELEVVSY DKKKHKAKLI GKDEKKDIAL ISFESDDATI KVADLGDSDK LEIGDWVMAV G SPFQFSFT ...String:
GPLGSSNRSN IVFAEEKDNT VRALQDSFRE VSKKILPSSV EVHATGVIKQ SFPIPFFFFD MPEFDSERKS NWAGSGVIIG RDSQKKSLF YVVTNSHVVD KATELEVVSY DKKKHKAKLI GKDEKKDIAL ISFESDDATI KVADLGDSDK LEIGDWVMAV G SPFQFSFT VTAGIVSGLQ RSANPNLQSR NLFIQTDAAI NRGNAGGPLV NIKGEVIGIN AWIASNSGGN IGLGFAIPVN NI KSTVDFF LKGKKIESAW LGISFYPLKT RDSEVLKSLG VESNDVSAAI IASLYPGSPA VKSGLRAGDI IMKVNGVSMS VFQ DVTSYI SDFYAGEKVN VEILRGNVKK NIEIVLAVRP KDKELSSSKM LPGFVVYPLV EDIKAQLNLR NWIKGVVVDY IDKN LASNI KMKSGDVILS VNSKSVSNLR EFYDALEVGK NTYKILRGND SFKITF

UniProtKB: Periplasmic serine protease DO

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Macromolecule #2: UNKNOWN fragment

MacromoleculeName: UNKNOWN fragment / type: protein_or_peptide / ID: 2
Details: 9 amino acids of unknown sequence modeled as alanine residues
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 783.958 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTris-HCLtris(hydroxymethyl)aminomethane hydrochloride
200.0 mMNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0003 kPa
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: OTHER / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsk3
CTF correctionSoftware - Name: cryoSPARC (ver. v4.4.1) / Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Alpha fold2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.4.1) / Number images used: 157066
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9zrj:
cryoEM structure of hexametric HtrA from Borrelia burgdorferi with bound peptides in the active sites

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