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- PDB-38ky: Cryo EM structure of a peroxidoxin from Trypanosoma brucei (reduc... -

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Basic information

Entry
Database: PDB / ID: 38ky
TitleCryo EM structure of a peroxidoxin from Trypanosoma brucei (reduced form)
Componentsperoxidoxin
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / peroxidoxin / Trypanosoma brucei
Function / homology
Function and homology information


tryparedoxin peroxidase activity / cellular response to antimycin A / trypanothione-disulfide reductase (NADPH) activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / regulation of mitochondrial membrane potential / hydrogen peroxide catabolic process / cellular response to heat / response to oxidative stress ...tryparedoxin peroxidase activity / cellular response to antimycin A / trypanothione-disulfide reductase (NADPH) activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / regulation of mitochondrial membrane potential / hydrogen peroxide catabolic process / cellular response to heat / response to oxidative stress / ciliary basal body / mitochondrion / cytosol
Similarity search - Function
Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
thioredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLanyi Lari, N. / Lovell, S. / Hammons, A.M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD03633 United States
CitationJournal: To Be Published
Title: Cryo EM structure of a peroxidoxin from Trypanosoma brucei (reduced form)
Authors: Lanyi Lari, N. / Lovell, S. / Hammons, A.M.
History
DepositionSep 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: peroxidoxin
B: peroxidoxin
C: peroxidoxin
D: peroxidoxin
E: peroxidoxin
F: peroxidoxin
G: peroxidoxin
H: peroxidoxin
I: peroxidoxin
J: peroxidoxin


Theoretical massNumber of molelcules
Total (without water)226,55910
Polymers226,55910
Non-polymers00
Water00
1


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

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Components

#1: Protein
peroxidoxin


Mass: 22655.912 Da / Num. of mol.: 10 / Fragment: T35-L226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: mTryP / Plasmid: TrbrA.01056.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GU47, thioredoxin-dependent peroxiredoxin
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Decameric complex of a peroxidoxin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 233 MDa / Experimental value: YES
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) / Plasmid: TrbrA.01056.a.B2
Buffer solutionpH: 7
Details: 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide
SpecimenConc.: 2.88 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 4D-STEM / Nominal magnification: 100000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 100 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON I (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4886
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansWidth: 4060 / Height: 4060

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Processing

EM software
IDNameVersionCategory
1cryoSPARC5particle selection
2EPUimage acquisition
4cryoSPARC5CTF correction
7UCSF ChimeraX1.12model fitting
9PHENIX2.2_6163model refinement
10cryoSPARC5initial Euler assignment
11cryoSPARC5classification
12cryoSPARC53D reconstruction
Image processingDetails: The selected images were high-pass filtered and normalized
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6118747
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 498572 / Num. of class averages: 77 / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingAccession code: AF-Q9GU47-F1 / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.18 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313570
ELECTRON MICROSCOPYf_angle_d0.56318370
ELECTRON MICROSCOPYf_dihedral_angle_d3.9721780
ELECTRON MICROSCOPYf_chiral_restr0.0472080
ELECTRON MICROSCOPYf_plane_restr0.0042350

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