[English] 日本語
Yorodumi
- EMDB-53573: Murine AA amyloid fibril morphology III (AA III) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53573
TitleMurine AA amyloid fibril morphology III (AA III)
Map data
Sample
  • Complex: Amyloid fibril containing SAA peptides
    • Protein or peptide: Serum amyloid A-2 protein
KeywordsAmyloid fibril / AA amyloidosis / systemic amyloidosis / AApoAII amyloidosis / misfolfing disease / protein aggregation / PROTEIN FIBRIL
Function / homologySerum amyloid A protein / : / Serum amyloid A protein / Serum amyloid A proteins signature. / Serum amyloid A proteins / response to stilbenoid / high-density lipoprotein particle / acute-phase response / Serum amyloid A-2 protein
Function and homology information
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsAndreotti G / Schmidt M / Faendrich M
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)1279/Z03 Germany
German Research Foundation (DFG)A03 Germany
CitationJournal: J Mol Biol / Year: 2025
Title: Cryo-EM Observation of AA Amyloid Fibrils in Mouse Model of Systemic AApoAII Amyloidosis.
Authors: Giada Andreotti / Keichii Higuchi / Matthias Schmidt / Marcus Fändrich /
Abstract: The co-deposition of amyloid fibrils from different precursor proteins is a topic of increasing relevance for protein misfolding diseases. Using cryo-electron microscopy (cryo-EM), we here determined ...The co-deposition of amyloid fibrils from different precursor proteins is a topic of increasing relevance for protein misfolding diseases. Using cryo-electron microscopy (cryo-EM), we here determined the structures of two serum amyloid A (SAA) protein-derived amyloid fibril morphologies that were extracted from a mouse strain that is primarily known to be associated with apolipoprotein A-II-derived amyloid fibrils. The two fibril morphologies show the same protomer conformation as in previously reported ex vivo amyloid fibrils from SAA protein but a different relative arrangement of fibril protein stacks. These data establish that serum amyloid A-derived amyloid fibrils share the same fibril protein fold in different mouse strains and disease contexts.
History
DepositionMay 8, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53573.png

Downloads & links

-
Map

FileDownload / File: emd_53573.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.042014923 - 0.07255008
Average (Standard dev.)0.00010530845 (±0.0016988923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53573_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_53573_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_53573_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_53573_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Amyloid fibril containing SAA peptides

EntireName: Amyloid fibril containing SAA peptides
Components
  • Complex: Amyloid fibril containing SAA peptides
    • Protein or peptide: Serum amyloid A-2 protein

-
Supramolecule #1: Amyloid fibril containing SAA peptides

SupramoleculeName: Amyloid fibril containing SAA peptides / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse) / Organ: liver

-
Macromolecule #1: Serum amyloid A-2 protein

MacromoleculeName: Serum amyloid A-2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.622629 KDa
SequenceString:
GFFSFIGEAF QGAGDMWRAY TDMKEAGWKD GDKYFHARGN YDAAQRGPGG VWAAEKISDA RESFQEFFGR GHEDTMADQE ANRHGRSGK DPNYYRPPGL PAKY

UniProtKB: Serum amyloid A-2 protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 7 / Details: water
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA PLUNGER

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.26 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 2034
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9r4z:
Murine AA amyloid fibril morphology III (AA III)

+
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