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- PDB-6mst: Cryo-EM structure of human AA amyloid fibril -

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Basic information

Entry
Database: PDB / ID: 6mst
TitleCryo-EM structure of human AA amyloid fibril
ComponentsSerum amyloid A-1 protein
KeywordsPROTEIN FIBRIL / AA-amyloidosis / Serum Amyloid A / cross-beta / helical
Function / homology
Function and homology information


Scavenging by Class B Receptors / positive regulation of interleukin-1 production / lymphocyte chemotaxis / high-density lipoprotein particle / Formyl peptide receptors bind formyl peptides and many other ligands / macrophage chemotaxis / regulation of protein secretion / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / positive regulation of cell adhesion ...Scavenging by Class B Receptors / positive regulation of interleukin-1 production / lymphocyte chemotaxis / high-density lipoprotein particle / Formyl peptide receptors bind formyl peptides and many other ligands / macrophage chemotaxis / regulation of protein secretion / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / positive regulation of cell adhesion / cytoplasmic microtubule / endocytic vesicle lumen / neutrophil chemotaxis / G protein-coupled receptor binding / positive regulation of cytokine production / acute-phase response / TAK1-dependent IKK and NF-kappa-B activation / negative regulation of inflammatory response / platelet activation / heparin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (q) signalling events / Interleukin-4 and Interleukin-13 signaling / Amyloid fiber formation / extracellular exosome / extracellular region
Similarity search - Function
Serum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / Serum amyloid A proteins
Similarity search - Domain/homology
Serum amyloid A-1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLoerch, S. / Rennegarbe, M. / Liberta, F. / Grigorieff, N. / Fandrich, M. / Schmidt, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG FA 456/15-1 Germany
German Research Foundation (DFG)DFG SCHM 3276/1 Germany
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 /
Abstract: Systemic AA amyloidosis is a worldwide occurring protein misfolding disease of humans and animals. It arises from the formation of amyloid fibrils from the acute phase protein serum amyloid A. Here, ...Systemic AA amyloidosis is a worldwide occurring protein misfolding disease of humans and animals. It arises from the formation of amyloid fibrils from the acute phase protein serum amyloid A. Here, we report the purification and electron cryo-microscopy analysis of amyloid fibrils from a mouse and a human patient with systemic AA amyloidosis. The obtained resolutions are 3.0 Å and 2.7 Å for the murine and human fibril, respectively. The two fibrils differ in fundamental properties, such as presence of right-hand or left-hand twisted cross-β sheets and overall fold of the fibril proteins. Yet, both proteins adopt highly similar β-arch conformations within the N-terminal ~21 residues. Our data demonstrate the importance of the fibril protein N-terminus for the stability of the analyzed amyloid fibril morphologies and suggest strategies of combating this disease by interfering with specific fibril polymorphs.
History
DepositionOct 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Serum amyloid A-1 protein
B: Serum amyloid A-1 protein
C: Serum amyloid A-1 protein
E: Serum amyloid A-1 protein
D: Serum amyloid A-1 protein
F: Serum amyloid A-1 protein
H: Serum amyloid A-1 protein
I: Serum amyloid A-1 protein
J: Serum amyloid A-1 protein
K: Serum amyloid A-1 protein
L: Serum amyloid A-1 protein
G: Serum amyloid A-1 protein


Theoretical massNumber of molelcules
Total (without water)89,77412
Polymers89,77412
Non-polymers00
Water0
1


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

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Components

#1: Protein
Serum amyloid A-1 protein / / SAA


Mass: 7481.154 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0DJI8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: human AA amyloid fibril / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Organ: kidney
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: 15 mA / Grid material: COPPER / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K

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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: 130000 X / Nominal defocus max: -2500 nm / Nominal defocus min: -500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 12 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2SerialEM3.5image acquisition
4Gctf1.06CTF correction
7PHENIX1.14-3219model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.14-3219model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0.79 ° / Axial rise/subunit: 2.4 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 93025
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91872 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL

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