[English] 日本語
Yorodumi
- EMDB-47645: Leishmania tarentolae 48 nm doublet microtubule protofilament 9.3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47645
TitleLeishmania tarentolae 48 nm doublet microtubule protofilament 9.3 focused refinement
Map dataDeepemhancer map of the Leishmania tarentolae 48 nm doublet microtubule protofilament 9.3 focused refinement
Sample
  • Complex: 48-nm structure of the Leishmania tarentolae doublet microtubule
Keywordsflagella / parasite / axoneme / doublet microtubule / STRUCTURAL PROTEIN
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDoran MH / Brown A
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141109 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143183 United States
CitationJournal: Science / Year: 2025
Title: Evolutionary adaptations of doublet microtubules in trypanosomatid parasites.
Authors: Matthew H Doran / Qingwei Niu / Jianwei Zeng / Tom Beneke / James Smith / Peter Ren / Sophia Fochler / Adrian Coscia / Johanna L Höög / Shimi Meleppattu / Polina V Lishko / Richard J ...Authors: Matthew H Doran / Qingwei Niu / Jianwei Zeng / Tom Beneke / James Smith / Peter Ren / Sophia Fochler / Adrian Coscia / Johanna L Höög / Shimi Meleppattu / Polina V Lishko / Richard J Wheeler / Eva Gluenz / Rui Zhang / Alan Brown /
Abstract: The movement and pathogenicity of trypanosomatid species, the causative agents of trypanosomiasis and leishmaniasis, are dependent on a flagellum that contains an axoneme of dynein-bound doublet ...The movement and pathogenicity of trypanosomatid species, the causative agents of trypanosomiasis and leishmaniasis, are dependent on a flagellum that contains an axoneme of dynein-bound doublet microtubules (DMTs). In this work, we present cryo-electron microscopy structures of DMTs from two trypanosomatid species, and , at resolutions up to 2.7 angstrom. The structures revealed 27 trypanosomatid-specific microtubule inner proteins, a specialized dynein-docking complex, and the presence of paralogous proteins that enable higher-order periodicities or proximal-distal patterning. Leveraging the genetic tractability of trypanosomatid species, we quantified the location and contribution of each structure-identified protein to swimming behavior. Our study shows that proper B-tubule closure is critical for flagellar motility, exemplifying how integrating structural identification with systematic gene deletion can dissect individual protein contributions to flagellar motility.
History
DepositionOct 31, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47645.png

Downloads & links

-
Map

FileDownload / File: emd_47645.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepemhancer map of the Leishmania tarentolae 48 nm doublet microtubule protofilament 9.3 focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 512 pix.
= 680.96 Å		1.33 Å/pix.
x 512 pix.
= 680.96 Å		1.33 Å/pix.
x 512 pix.
= 680.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0076802652 - 2.293485
Average (Standard dev.)0.0004965341 (±0.01659897)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 680.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Relion postprocessed map of the Leishmania tarentolae 48...

Fileemd_47645_additional_1.map
AnnotationRelion postprocessed map of the Leishmania tarentolae 48 nm doublet microtubule protofilament 9.3 focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Relion reconstruction of the Leishmania tarentolae 48 nm...

Fileemd_47645_additional_2.map
AnnotationRelion reconstruction of the Leishmania tarentolae 48 nm doublet microtubule protofilament 9.3 focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 of the Leishmania tarentolae 48...

Fileemd_47645_half_map_1.map
AnnotationHalf map 1 of the Leishmania tarentolae 48 nm doublet microtubule protofilament 9.3 focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 of the Leishmania tarentolae 48...

Fileemd_47645_half_map_2.map
AnnotationHalf map 2 of the Leishmania tarentolae 48 nm doublet microtubule protofilament 9.3 focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 48-nm structure of the Leishmania tarentolae doublet microtubule

EntireName: 48-nm structure of the Leishmania tarentolae doublet microtubule
Components
  • Complex: 48-nm structure of the Leishmania tarentolae doublet microtubule

-
Supramolecule #1: 48-nm structure of the Leishmania tarentolae doublet microtubule

SupramoleculeName: 48-nm structure of the Leishmania tarentolae doublet microtubule
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#86
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Organelle: Flagella

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

Concentration6.5 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample consisted of freshly splayed Leishmania tarentolae axonemes.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

20631


Details: The map used for initial angular assignment is the C. reinhardtii DMT.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 533420
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: integrative model
Details: The initial model consisted of rigid body fit AlphaFold models and models build with ModelAngelo.

+
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