[English] 日本語
Yorodumi
- EMDB-78897: Cryo EM structure of a peroxidoxin from Trypanosoma brucei (reduc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-78897
TitleCryo EM structure of a peroxidoxin from Trypanosoma brucei (reduced form)
Map data
Sample
  • Complex: Decameric complex of a peroxidoxin
    • Protein or peptide: peroxidoxin
KeywordsSSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / peroxidoxin / Trypanosoma brucei / OXIDOREDUCTASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLanyi Lari N / Lovell S / Hammons AM / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2 items
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 AM
History
DepositionSep 1, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_78897.png

Downloads & links

-
Map

FileDownload / File: emd_78897.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 256 pix.
= 302.08 Å		1.18 Å/pix.
x 256 pix.
= 302.08 Å		1.18 Å/pix.
x 256 pix.
= 302.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.046
Minimum - Maximum-0.080473855 - 0.19302002
Average (Standard dev.)0.0006333394 (±0.005727723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 302.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_78897_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_78897_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_78897_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Decameric complex of a peroxidoxin

EntireName: Decameric complex of a peroxidoxin
Components
  • Complex: Decameric complex of a peroxidoxin
    • Protein or peptide: peroxidoxin

-
Supramolecule #1: Decameric complex of a peroxidoxin

SupramoleculeName: Decameric complex of a peroxidoxin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote)
Molecular weightTheoretical: 233 MDa

-
Macromolecule #1: peroxidoxin

MacromoleculeName: peroxidoxin / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: thioredoxin-dependent peroxiredoxin
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote)
Molecular weightTheoretical: 22.655912 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAHHHHHHTA TVREAAPEFA GKAVVDGKIK DISMNDYKGK YIVLFFYPLD FTFVCPTEIV SFSDSHAEFE KLNTQVIAVS CDSHFSHLA WVETPRKKGG LGEMKIPLLS DFTKEISRDY GVLVEEQGLS LRALFVIDDK GILRHVTIND LPVGRNVDEV L RVVQAFQY ...String:
MAHHHHHHTA TVREAAPEFA GKAVVDGKIK DISMNDYKGK YIVLFFYPLD FTFVCPTEIV SFSDSHAEFE KLNTQVIAVS CDSHFSHLA WVETPRKKGG LGEMKIPLLS DFTKEISRDY GVLVEEQGLS LRALFVIDDK GILRHVTIND LPVGRNVDEV L RVVQAFQY ADKTGDVIPC NWKPGKETMK VEAAKEYFEK NL

UniProtKB: thioredoxin-dependent peroxiredoxin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

-
Sample preparation

Concentration2.88 mg/mL
BufferpH: 7
Details: 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 1 sec. / Pretreatment - Pressure: 0.005 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4060 pixel / Digitization - Dimensions - Height: 4060 pixel / Number grids imaged: 1 / Number real images: 4886 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

DetailsThe selected images were high-pass filtered and normalized
Particle selectionNumber selected: 6118747
CTF correctionSoftware - Name: cryoSPARC (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AF-Q9GU47-F1
Final reconstructionNumber classes used: 77 / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0) / Number images used: 498572
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 200 / Software - Name: cryoSPARC (ver. 5.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.12)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-38ky:
Cryo EM structure of a peroxidoxin from Trypanosoma brucei (reduced form)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more