[English] 日本語
Yorodumi
- EMDB-62570: Cryo-EM structure of the TIA-1 prion-like domain amyloid fibril, WT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62570
TitleCryo-EM structure of the TIA-1 prion-like domain amyloid fibril, WT
Map data
Sample
  • Complex: Amyloid fibril formed by TIA-1 prion-like domain
    • Protein or peptide: Cytotoxic granule associated RNA binding protein TIA1
KeywordsAmyloid fibril / Prion-like domain / RNA-binding protein / PROTEIN FIBRIL
Function / homology
Function and homology information


protein localization to cytoplasmic stress granule / nuclear stress granule / poly(A) binding / mRNA 3'-UTR AU-rich region binding / regulation of mRNA splicing, via spliceosome / positive regulation of epithelial cell apoptotic process / FGFR2 alternative splicing / negative regulation of cytokine production / regulation of alternative mRNA splicing, via spliceosome / stress granule assembly ...protein localization to cytoplasmic stress granule / nuclear stress granule / poly(A) binding / mRNA 3'-UTR AU-rich region binding / regulation of mRNA splicing, via spliceosome / positive regulation of epithelial cell apoptotic process / FGFR2 alternative splicing / negative regulation of cytokine production / regulation of alternative mRNA splicing, via spliceosome / stress granule assembly / RNA splicing / mRNA 3'-UTR binding / mRNA processing / cytoplasmic stress granule / negative regulation of translation / ribonucleoprotein complex / apoptotic process / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
TIA-1, RNA recognition motif 1 / TIA-1, RNA recognition motif 2 / TIAR, RNA recognition motif 3 / RNA recognition motif domain, eukaryote / RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Cytotoxic granule associated RNA binding protein TIA1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsInaoka D / Miyata T / Makino F / Ohtani Y / Ekari M / Kobayashi R / Imamura K / Sakamoto E / Kodama ST / Yoshida N ...Inaoka D / Miyata T / Makino F / Ohtani Y / Ekari M / Kobayashi R / Imamura K / Sakamoto E / Kodama ST / Yoshida N / Kato T / Namba K / Tochio H / Sekiyama N
Funding support Japan, 2 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP22H05090 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121003 Japan
CitationJournal: To Be Published
Title: TIA-1 PLD amyloid fibril formation is suppressed by the ALS-associated mutation
Authors: Inaoka D / Miyata T / Makino F / Ohtani Y / Ekari M / Kobayashi R / Imamura K / Sakamoto E / Kodama ST / Yoshida N / Kato T / Namba K / Tochio H / Sekiyama N
History
DepositionDec 3, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62570.png

Downloads & links

-
Map

FileDownload / File: emd_62570.map.gz / Format: CCP4 / Size: 347.6 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 Å/pix.
x 450 pix.
= 450. Å		1 Å/pix.
x 450 pix.
= 450. Å		1 Å/pix.
x 450 pix.
= 450. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.014952949 - 0.02774422
Average (Standard dev.)0.000011137963 (±0.00040079487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 450.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_62570_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62570_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Amyloid fibril formed by TIA-1 prion-like domain

EntireName: Amyloid fibril formed by TIA-1 prion-like domain
Components
  • Complex: Amyloid fibril formed by TIA-1 prion-like domain
    • Protein or peptide: Cytotoxic granule associated RNA binding protein TIA1

-
Supramolecule #1: Amyloid fibril formed by TIA-1 prion-like domain

SupramoleculeName: Amyloid fibril formed by TIA-1 prion-like domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Cytotoxic granule associated RNA binding protein TIA1

MacromoleculeName: Cytotoxic granule associated RNA binding protein TIA1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.345128 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH HHHHHHSENL YFQGGQYMPN GWQVPAYGMY GQAWNQQGFN QTQSSAPWMG PNYGVQPPQG QNGSMLPNQP SGYRVAGYE TQ

UniProtKB: Cytotoxic granule associated RNA binding protein TIA1

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 2 / Component - Concentration: 0.1 % / Component - Formula: CF3COOH / Component - Name: Trifluoroacetic acid
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 4650 / Average exposure time: 5.353 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.38 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.37 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 56747
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 610417 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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