[English] 日本語
Yorodumi
- EMDB-5305: Trypanosoma brucei flagellum: connector 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5305
TitleTrypanosoma brucei flagellum: connector 2
Map dataSub-tomogram average of the Trypanosoma brucei connector 2. Some density belonging to microtubule doublet number 5, with which this connector is associated, also appears.
Sample
  • Sample: Trypanosoma brucei flagellum - connector 2
  • Organelle or cellular component: connector 2
Keywordsconnector 2
Biological speciesTrypanosoma brucei (eukaryote)
Methodsubtomogram averaging / cryo EM
AuthorsKoyfman AY / Schmid MF / Gheiratmand L / Fu CJ / Khant HA / Huang D / He CY / Chiu W
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Structure of Trypanosoma brucei flagellum accounts for its bihelical motion.
Authors: Alexey Y Koyfman / Michael F Schmid / Ladan Gheiratmand / Caroline J Fu / Htet A Khant / Dandan Huang / Cynthia Y He / Wah Chiu /
Abstract: Trypanosoma brucei is a parasitic protozoan that causes African sleeping sickness. It contains a flagellum required for locomotion and viability. In addition to a microtubular axoneme, the flagellum ...Trypanosoma brucei is a parasitic protozoan that causes African sleeping sickness. It contains a flagellum required for locomotion and viability. In addition to a microtubular axoneme, the flagellum contains a crystalline paraflagellar rod (PFR) and connecting proteins. We show here, by cryoelectron tomography, the structure of the flagellum in three bending states. The PFR lattice in straight flagella repeats every 56 nm along the length of the axoneme, matching the spacing of the connecting proteins. During flagellar bending, the PFR crystallographic unit cell lengths remain constant while the interaxial angles vary, similar to a jackscrew. The axoneme drives the expansion and compression of the PFR lattice. We propose that the PFR modifies the in-plane axoneme motion to produce the characteristic trypanosome bihelical motility as captured by high-speed light microscope videography.
History
DepositionJun 8, 2011-
Header (metadata) releaseJun 21, 2011-
Map releaseJun 21, 2011-
UpdateJun 5, 2013-
Current statusJun 5, 2013Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_5305.map.gz / Format: CCP4 / Size: 2.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of the Trypanosoma brucei connector 2. Some density belonging to microtubule doublet number 5, with which this connector is associated, also appears.
Voxel sizeX=Y=Z: 10.686 Å
Density
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-2.48806715 - 4.41671705
Average (Standard dev.)-0.11527341 (±0.797315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin11-170-122
Dimensions6416064
Spacing6416064
CellA: 1709.76 Å / B: 683.904 Å / C: 683.904 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.68610.68610.686
M x/y/z1606464
origin x/y/z0.0000.0000.000
length x/y/z1709.760683.904683.904
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-17011-122
NC/NR/NS1606464
D min/max/mean-2.4884.417-0.115

-
Supplemental data

-
Sample components

-
Entire : Trypanosoma brucei flagellum - connector 2

EntireName: Trypanosoma brucei flagellum - connector 2
Components
  • Sample: Trypanosoma brucei flagellum - connector 2
  • Organelle or cellular component: connector 2

-
Supramolecule #1000: Trypanosoma brucei flagellum - connector 2

SupramoleculeName: Trypanosoma brucei flagellum - connector 2 / type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: connector 2

SupramoleculeName: connector 2 / type: organelle_or_cellular_component / ID: 1 / Name.synonym: connector 2 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Trypanosoma brucei (eukaryote) / synonym: Trypanosome / Organelle: flagellum / Location in cell: flagellum

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging

-
Sample preparation

BufferDetails: PBS
GridDetails: 200 mesh gold grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: Vitrobot III / Method: Blot for 2 seconds before plunging

-
Electron microscopy

MicroscopeJEOL 2100
DateJun 25, 2008
Image recordingAverage electron dose: 70 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 15000
Sample stageSpecimen holder: 60 degree / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °

-
Image processing

DetailsAverage number of tilts used in the 3D reconstructions: 60. Average tomographic tilt angle increment: 2.
Final reconstructionSoftware - Name: IMOD

+
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://pdbjlvh1.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