[English] 日本語
Yorodumi
- EMDB-66706: Cryo-EM structure of Sup35NM fibril formed at 4 degrees (Sc4) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66706
TitleCryo-EM structure of Sup35NM fibril formed at 4 degrees (Sc4)
Map data
Sample
  • Complex: Amyloid fibril of Sup35NM Sc4
    • Protein or peptide: Eukaryotic peptide chain release factor GTP-binding subunit
KeywordsYeast / Sup35NM / Amyloid / PROTEIN FIBRIL
Function / homology
Function and homology information


Eukaryotic Translation Termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / cytoplasmic stress granule / regulation of translation / ribosome binding ...Eukaryotic Translation Termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / cytoplasmic stress granule / regulation of translation / ribosome binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / mRNA binding / GTPase activity / GTP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Eukaryotic peptide chain release factor GTP-binding subunit / : / GTP-eEF1A C-terminal domain-like / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain ...Eukaryotic peptide chain release factor GTP-binding subunit / : / GTP-eEF1A C-terminal domain-like / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Eukaryotic peptide chain release factor GTP-binding subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNomura T / Boyer DR / Tanaka M
Funding support Japan, France, United States, 11 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)21gm1410009 Japan
Japan Society for the Promotion of Science (JSPS)20H00501 Japan
Japan Society for the Promotion of Science (JSPS)24H00603 Japan
Japan Society for the Promotion of Science (JSPS)21H05257 Japan
Human Frontier Science Program (HFSP)RGP0010/2011 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM032543 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG048120 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG070895 United States
Japan Society for the Promotion of Science (JSPS)22K15067 Japan
Japan Society for the Promotion of Science (JSPS)JP25830025 Japan
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R24GM154186 United States
CitationJournal: Res Sq / Year: 2025
Title: How Sup35 monomer conformation and amyloid fibril polymorphism determine yeast strain phenotypes.
Authors: Motomasa Tanaka / Takashi Nomura / David Boyer / Yusuke Komi / Peng Ge / Rodrigo A Maillard / Piere Rodriguez / Atsushi Yamagata / Mikako Shirouzu / Giuseppe Legname / Bruno Samori / David Eisenberg /
Abstract: In the [ ] prion system, the yeast prion protein Sup35 can form structurally distinct amyloid fibrils that lead to distinct transmissible prion states, or strains. However, our understanding of how ...In the [ ] prion system, the yeast prion protein Sup35 can form structurally distinct amyloid fibrils that lead to distinct transmissible prion states, or strains. However, our understanding of how different Sup35 fibril structures arise and translate to phenotypic variations is limited. Here, using cryo-EM and single-monomer force spectroscopy with optical tweezers, we reveal the structural basis of yeast prion propagation in four wild-type and S17R mutant variants of Sup35 that underlie different [ ] strains. Cryo-EM structures show that the four variants form strikingly distinct fibril structures, which exhibit varying stability and chaperone-accessibility. Force spectroscopy suggests the different distinct fibril structures are derived from distinct monomer conformational ensembles. Further, cryo-EM structures indicate that prion strain strength is correlated with enhanced fibril propagation caused by a combination of low fibril stability and a large separation between the Sup35 fibril core and the Ssa1/Sis1 chaperone-binding region. These results provide a structure-based mechanism for the yeast prion strain phenomenon with implications for understanding amyloid propagation in human neurodegenerative diseases.
History
DepositionOct 24, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_66706.png

Downloads & links

-
Map

FileDownload / File: emd_66706.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 160 pix.
= 172.48 Å		1.08 Å/pix.
x 160 pix.
= 172.48 Å		1.08 Å/pix.
x 160 pix.
= 172.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.73
Minimum - Maximum-10.817304 - 18.9132
Average (Standard dev.)-0.000000034302715 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 172.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_66706_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_66706_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Amyloid fibril of Sup35NM Sc4

EntireName: Amyloid fibril of Sup35NM Sc4
Components
  • Complex: Amyloid fibril of Sup35NM Sc4
    • Protein or peptide: Eukaryotic peptide chain release factor GTP-binding subunit

-
Supramolecule #1: Amyloid fibril of Sup35NM Sc4

SupramoleculeName: Amyloid fibril of Sup35NM Sc4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Macromolecule #1: Eukaryotic peptide chain release factor GTP-binding subunit

MacromoleculeName: Eukaryotic peptide chain release factor GTP-binding subunit
type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 29.513445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDSNQGNNQ QNYQQYSQNG NQQQGNNRYQ GYQAYNAQAQ PAGGYYQNYQ GYSGYQQGGY QQYNPDAGYQ QQYNPQGGYQ QYNPQGGYQ QQFNPQGGRG NYKNFNYNNN LQGYQAGFQP QSQGMSLNDF QKQQKQAAPK PKKTLKLVSS SGIKLANATK K VGTKPAES ...String:
MSDSNQGNNQ QNYQQYSQNG NQQQGNNRYQ GYQAYNAQAQ PAGGYYQNYQ GYSGYQQGGY QQYNPDAGYQ QQYNPQGGYQ QYNPQGGYQ QQFNPQGGRG NYKNFNYNNN LQGYQAGFQP QSQGMSLNDF QKQQKQAAPK PKKTLKLVSS SGIKLANATK K VGTKPAES DKKEEEKSAE TKEPTKEPTK VEEPVKKEEK PVQTEEKTEE KSELPKVEDL KISESTHNTN NANVTSADAL IK EQEEEVD DEVVNDHHHH HHH

UniProtKB: Eukaryotic peptide chain release factor GTP-binding subunit

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.5 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.83 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.82 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 86542
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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