[English] 日本語
Yorodumi
- PDB-7tns: Subpellicular microtubule from detergent-extract Toxoplasma gondi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tns
TitleSubpellicular microtubule from detergent-extract Toxoplasma gondii cells
Components
  • (PDI family protein) x 2
  • Microtubule associated protein SPM1
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL INVASION / parasites / Toxoplasma gondii / cytoskeleton / microtubules / tubulin
Function / homology
Function and homology information


protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule binding / microtubule / hydrolase activity / GTPase activity / GTP binding ...protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule binding / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Stabilizer of axonemal microtubules 1/2 / Thioredoxin-like / Thioredoxin-like fold / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain ...Stabilizer of axonemal microtubules 1/2 / Thioredoxin-like / Thioredoxin-like fold / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
PDI family protein / PDI family protein / Tubulin beta chain / Tubulin alpha chain / Microtubule associated protein SPM1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.7 Å
AuthorsSun, S.Y. / Pintilie, G.D. / Chen, M. / Chiu, W.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD021600 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM121203 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21MH125285-01A1 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Cryo-ET of parasites gives subnanometer insight into tubulin-based structures.
Authors: Stella Y Sun / Li-Av Segev-Zarko / Muyuan Chen / Grigore D Pintilie / Michael F Schmid / Steven J Ludtke / John C Boothroyd / Wah Chiu /
Abstract: Tubulin is a conserved protein that polymerizes into different forms of filamentous structures in , an obligate intracellular parasite in the phylum Apicomplexa. Two key tubulin-containing ...Tubulin is a conserved protein that polymerizes into different forms of filamentous structures in , an obligate intracellular parasite in the phylum Apicomplexa. Two key tubulin-containing cytoskeletal components are subpellicular microtubules (SPMTs) and conoid fibrils (CFs). The SPMTs help maintain shape and gliding motility, while the CFs are implicated in invasion. Here, we use cryogenic electron tomography to determine the molecular structures of the SPMTs and CFs in vitrified intact and detergent-extracted parasites. Subvolume densities from detergent-extracted parasites yielded averaged density maps at subnanometer resolutions, and these were related back to their architecture in situ. An intralumenal spiral lines the interior of the 13-protofilament SPMTs, revealing a preferred orientation of these microtubules relative to the parasite's long axis. Each CF is composed of nine tubulin protofilaments that display a comma-shaped cross-section, plus additional associated components. Conoid protrusion, a crucial step in invasion, is associated with an altered pitch of each CF. The use of basic building blocks of protofilaments and different accessory proteins in one organism illustrates the versatility of tubulin to form two distinct types of assemblies, SPMTs and CFs.
History
DepositionJan 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: Microtubule associated protein SPM1
1: Microtubule associated protein SPM1
10: Microtubule associated protein SPM1
11: Microtubule associated protein SPM1
12: Microtubule associated protein SPM1
13: Microtubule associated protein SPM1
14: Microtubule associated protein SPM1
15: Microtubule associated protein SPM1
16: Microtubule associated protein SPM1
17: Microtubule associated protein SPM1
18: Microtubule associated protein SPM1
19: Microtubule associated protein SPM1
2: Microtubule associated protein SPM1
20: Microtubule associated protein SPM1
21: Microtubule associated protein SPM1
22: Microtubule associated protein SPM1
23: Microtubule associated protein SPM1
3: Microtubule associated protein SPM1
4: Microtubule associated protein SPM1
5: Microtubule associated protein SPM1
6: Microtubule associated protein SPM1
7: Microtubule associated protein SPM1
8: Microtubule associated protein SPM1
9: Microtubule associated protein SPM1
A0: Tubulin alpha chain
A1: Tubulin beta chain
A2: Tubulin alpha chain
A3: Tubulin beta chain
A4: Tubulin alpha chain
A5: Tubulin beta chain
A6: Tubulin alpha chain
A7: Tubulin beta chain
A8: Tubulin alpha chain
A9: Tubulin beta chain
B0: Tubulin alpha chain
B1: Tubulin beta chain
B2: Tubulin alpha chain
B3: Tubulin beta chain
B4: Tubulin alpha chain
B5: Tubulin beta chain
B6: Tubulin alpha chain
B7: Tubulin beta chain
B8: Tubulin alpha chain
B9: Tubulin beta chain
C0: Tubulin alpha chain
C1: Tubulin beta chain
C2: Tubulin alpha chain
C3: Tubulin beta chain
C4: Tubulin alpha chain
C5: Tubulin beta chain
C6: Tubulin alpha chain
C7: Tubulin beta chain
C8: Tubulin alpha chain
C9: Tubulin beta chain
D0: Tubulin alpha chain
D1: Tubulin beta chain
D2: Tubulin alpha chain
D3: Tubulin beta chain
D4: Tubulin alpha chain
D5: Tubulin beta chain
D6: Tubulin alpha chain
D7: Tubulin beta chain
D8: Tubulin alpha chain
D9: Tubulin beta chain
E0: Tubulin alpha chain
E1: Tubulin beta chain
E2: Tubulin alpha chain
E3: Tubulin beta chain
E4: Tubulin alpha chain
E5: Tubulin beta chain
E6: Tubulin alpha chain
E7: Tubulin beta chain
E8: Tubulin alpha chain
E9: Tubulin beta chain
F0: Tubulin alpha chain
F1: Tubulin beta chain
a: PDI family protein
b: PDI family protein
c: PDI family protein
d: PDI family protein
e: PDI family protein
f: PDI family protein
g: PDI family protein
h: PDI family protein
i: PDI family protein
j: PDI family protein
k: PDI family protein
l: PDI family protein
m: PDI family protein
n: PDI family protein
o: PDI family protein
p: PDI family protein
q: PDI family protein
r: PDI family protein
s: PDI family protein
t: PDI family protein
u: PDI family protein
v: PDI family protein
w: PDI family protein
x: PDI family protein
y: PDI family protein


Theoretical massNumber of molelcules
Total (without water)4,159,287101
Polymers4,159,287101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
Microtubule associated protein SPM1


Mass: 38817.699 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / Strain: ATCC 50611 / Me49 / References: UniProt: S8F1Y1
#2: Protein ...
Tubulin alpha chain / Alpha-tubulin


Mass: 50166.645 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / Strain: ME49 / References: UniProt: P10873
#3: Protein ...
Tubulin beta chain


Mass: 50119.121 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / Strain: ATCC 50611 / Me49 / References: UniProt: A0A125YWG5
#4: Protein ...
PDI family protein


Mass: 24939.332 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / Strain: ATCC 50611 / Me49
References: UniProt: A0A125YMM3, protein-disulfide reductase
#5: Protein PDI family protein


Mass: 21687.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / Strain: ATCC 50611 / Me49 / References: UniProt: A0A125YFI4
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: microtubule complex of alpha-tubulin and beta-tubulin with intra-lumenal proteins
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Toxoplasma gondii (eukaryote) / Strain: ME49
Buffer solutionpH: 7.2 / Details: Phosphate-Buffered Saline
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Homemade
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 295 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 4.2 e/Å2 / Avg electron dose per subtomogram: 132 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 6

-
Processing

EM software
IDNameVersionCategory
4EMAN2CTF correction
7UCSF Chimera1.13model fitting
12EMAN23D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 27.7 ° / Axial rise/subunit: 80 Å / Axial symmetry: C13
3D reconstructionResolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39122 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
EM volume selectionNum. of tomograms: 90 / Num. of volumes extracted: 39122
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7MIZ

7miz

+
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