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- EMDB-23619: Sub-tomographic averaged structure of the paracrystalline PFR dis... -

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Entry
Database: EMDB / ID: EMD-23619
TitleSub-tomographic averaged structure of the paracrystalline PFR distal zone in T. brucei
Map dataThe unmasked sub-tomographic averaging result of the PFR distal zone of T. brucei, after low pass filtering to 30 Angstrom
Sample
  • Organelle or cellular component: Sub-tomographic averaged structure of the paracrystalline PFR distal zone in T. brucei
Biological speciesTrypanosoma brucei brucei (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 28.5 Å
AuthorsZhang J / Wang H
Funding support United States, Switzerland, 10 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI052348 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DE028583 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
Swiss National Science FoundationP300PA_174358 Switzerland
Swiss National Science FoundationP2BEP3_162094 Switzerland
CitationJournal: Cell Discov / Year: 2021
Title: Structure of the trypanosome paraflagellar rod and insights into non-planar motility of eukaryotic cells.
Authors: Jiayan Zhang / Hui Wang / Simon Imhof / Xueting Zhou / Shiqing Liao / Ivo Atanasov / Wong H Hui / Kent L Hill / Z Hong Zhou /
Abstract: Eukaryotic flagella (synonymous with cilia) rely on a microtubule-based axoneme, together with accessory filaments to carryout motility and signaling functions. While axoneme structures are well ...Eukaryotic flagella (synonymous with cilia) rely on a microtubule-based axoneme, together with accessory filaments to carryout motility and signaling functions. While axoneme structures are well characterized, 3D ultrastructure of accessory filaments and their axoneme interface are mostly unknown, presenting a critical gap in understanding structural foundations of eukaryotic flagella. In the flagellum of the protozoan parasite Trypanosoma brucei (T. brucei), the axoneme is accompanied by a paraflagellar rod (PFR) that supports non-planar motility and signaling necessary for disease transmission and pathogenesis. Here, we employed cryogenic electron tomography (cryoET) with sub-tomographic averaging, to obtain structures of the PFR, PFR-axoneme connectors (PACs), and the axonemal central pair complex (CPC). The structures resolve how the 8 nm repeat of the axonemal tubulin dimer interfaces with the 54 nm repeat of the PFR, which consist of proximal, intermediate, and distal zones. In the distal zone, stacked "density scissors" connect with one another to form a "scissors stack network (SSN)" plane oriented 45° to the axoneme axis; and ~370 parallel SSN planes are connected by helix-rich wires into a paracrystalline array with ~90% empty space. Connections from these wires to the intermediate zone, then to overlapping layers of the proximal zone and to the PACs, and ultimately to the CPC, point to a contiguous pathway for signal transmission. Together, our findings provide insights into flagellum-driven, non-planar helical motility of T. brucei and have broad implications ranging from cell motility and tensegrity in biology, to engineering principles in bionics.
History
DepositionMar 14, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23619.png

Downloads & links

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Map

FileDownload / File: emd_23619.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe unmasked sub-tomographic averaging result of the PFR distal zone of T. brucei, after low pass filtering to 30 Angstrom
Voxel sizeX=Y=Z: 5.106 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-8.53965 - 12.48058
Average (Standard dev.)2.9811284e-07 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-208-208-208
Dimensions416416416
Spacing416416416
CellA=B=C: 2124.096 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.1065.1065.106
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z2124.0962124.0962124.096
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS-208-208-208
NC/NR/NS416416416
D min/max/mean-8.54012.4810.000

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Supplemental data

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Sample components

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Entire : Sub-tomographic averaged structure of the paracrystalline PFR dis...

EntireName: Sub-tomographic averaged structure of the paracrystalline PFR distal zone in T. brucei
Components
  • Organelle or cellular component: Sub-tomographic averaged structure of the paracrystalline PFR distal zone in T. brucei

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Supramolecule #1: Sub-tomographic averaged structure of the paracrystalline PFR dis...

SupramoleculeName: Sub-tomographic averaged structure of the paracrystalline PFR distal zone in T. brucei
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Organelle: Flagellum

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 12 / Number images used: 1362
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 28.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1362

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