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- PDB-10br: Crystal structure of B. burgdorferi HtrA PDZ1-2 domains -

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Basic information

Entry
Database: PDB / ID: 10br
TitleCrystal structure of B. burgdorferi HtrA PDZ1-2 domains
ComponentsPeriplasmic serine protease DO
KeywordsHYDROLASE / HtrA / chaperone / PDZ domain / dimer
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 B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsShakya, A.K. / Herzberg, O. / Gallager, D.T.
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
DepositionJan 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)89,5314
Polymers89,5314
Non-polymers00
Water20,1591119
1
A: Periplasmic serine protease DO
B: Periplasmic serine protease DO


Theoretical massNumber of molelcules
Total (without water)44,7662
Polymers44,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Periplasmic serine protease DO
D: Periplasmic serine protease DO


Theoretical massNumber of molelcules
Total (without water)44,7662
Polymers44,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.025, 72.285, 76.968
Angle α, β, γ (deg.)65.35, 89.96, 89.19
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Periplasmic serine protease DO


Mass: 22382.814 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN THAT WAS CLEAVED WITH PRECISION PROTEASE LEAVING A GPLGS PENTPEPTIDE AT THE N-TERMINUS CORRESPONDING TO THE CLEAVAGE AND BAMH1 SITES.
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Strain: B31 / Gene: BB_0104 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51131
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M potassium thiocyanate and 30% polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 111596 / % possible obs: 98.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 1.61 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7615 / CC1/2: 0.554 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.502 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22961 5996 5.1 %RANDOM
Rwork0.18211 ---
obs0.18431 111596 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.764 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å2-0.08 Å20.12 Å2
2--1.14 Å2-0.03 Å2
3----1.57 Å2
Refinement stepCycle: 1 / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6114 0 0 1119 7233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126249
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.6158491
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56223.284268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.634151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5791528
X-RAY DIFFRACTIONr_chiral_restr0.1260.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024620
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6081.8933234
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5132.8314039
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4832.1113015
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.47930.24510129
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 435 -
Rwork0.289 7615 -
obs--91.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.24280.17210.36290.25610.44710.89260.01430.00780.02110.0149-0.0028-0.01370.07440.0177-0.01150.02720.0099-0.00160.00450.00370.04423.106110.087415.1488
20.1436-0.0122-0.10180.14950.33490.8015-0.00990.0071-0.0334-0.0245-0.0152-0.0013-0.0646-0.04740.02510.03270.0267-0.00320.02920.00240.02493.7216-6.7053-17.4705
30.16720.04030.11650.13950.4011.168-0.034-0.0150.0380.0392-0.00910.01030.1199-0.01010.04310.02910.00530.00110.01690.0060.025921.8536-7.488453.7928
40.4923-0.2329-0.36670.16120.31130.66470.00210.00240.0054-0.01210.0069-0.0101-0.04740.0187-0.0090.0168-0.0007-0.00290.00140.00060.05433.4763-24.251921.5428
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A271 - 474
2X-RAY DIFFRACTION2B276 - 474
3X-RAY DIFFRACTION3C276 - 474
4X-RAY DIFFRACTION4D271 - 474

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