[English] 日本語
Yorodumi
- PDB-6dso: Cryo-EM structure of murine AA amyloid fibril -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6dso
TitleCryo-EM structure of murine AA amyloid fibril
ComponentsSerum amyloid A-2 protein
KeywordsPROTEIN FIBRIL / AA-amyloidosis / fibril / cross-beta / helical
Function / homologySerum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / response to stilbenoid / high-density lipoprotein particle / cytoplasmic microtubule / G protein-coupled receptor binding / chemoattractant activity / cell chemotaxis / acute-phase response ...Serum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / response to stilbenoid / high-density lipoprotein particle / cytoplasmic microtubule / G protein-coupled receptor binding / chemoattractant activity / cell chemotaxis / acute-phase response / extracellular space / Serum amyloid A-2 protein
Function and homology information
Specimen sourceMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3 Å resolution
AuthorsLoerch, S. / Liberta, F. / Grigorieff, N. / Fandrich, M. / Schmidt, M.
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM fibril structures from systemic AA amyloidosis reveal the species complementarity of pathological amyloids.
Authors: Falk Liberta / Sarah Loerch / Matthies Rennegarbe / Angelika Schierhorn / Per Westermark / Gunilla T Westermark / Bouke P C Hazenberg / Nikolaus Grigorieff / Marcus Fändrich / Matthias Schmidt
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 14, 2018 / Release: Mar 13, 2019

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8910
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8910
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serum amyloid A-2 protein
B: Serum amyloid A-2 protein
C: Serum amyloid A-2 protein
D: Serum amyloid A-2 protein
E: Serum amyloid A-2 protein
F: Serum amyloid A-2 protein
G: Serum amyloid A-2 protein
H: Serum amyloid A-2 protein
I: Serum amyloid A-2 protein
J: Serum amyloid A-2 protein
K: Serum amyloid A-2 protein
L: Serum amyloid A-2 protein


Theoretical massNumber of molelcules
Total (without water)112,34512
Polyers112,34512
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)60940
ΔGint (kcal/M)-188
Surface area (Å2)28080
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 12 / Rise per n subunits: 2.41 Å / Rotation per n subunits: 179.44 deg.

-
Components

#1: Protein/peptide
Serum amyloid A-2 protein /


Mass: 9362.094 Da / Num. of mol.: 12 / Source: (natural) Mus musculus (house mouse) / References: UniProt: P05367

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: AA amyloid fibril / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organ: spleen / Organism: Mus musculus (house mouse)
Buffer solutionpH: 7
Buffer componentFormula: ddH2O
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20 mA, 0.25 mBar / Grid material: COPPER / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / Nominal defocus max: -5500 nm / Nominal defocus min: -1300 nm / Cs: 2.7 mm / C2 aperture diameter: 50 microns
Image recordingElectron dose: 2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 1063
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 40

-
Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2SerialEM3.5image acquisition
4Gctf1.06CTF correction
7PHENIX1.12-2829model fitting
9PHENIX1.12-2829model refinement
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.44 deg. / Axial rise/subunit: 2.41 Å / Axial symmetry: C1
Particle selectionNumber of particles selected: 137956
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 21024 / Symmetry type: HELICAL
Atomic model buildingRef protocol: AB INITIO MODEL

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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