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- PDB-6z1o: AL amyloid fibril from a lambda 3 light chain in conformation A -

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Entry
Database: PDB / ID: 6z1o
TitleAL amyloid fibril from a lambda 3 light chain in conformation A
Componentslambda 3 immunoglobulin light chain fragment, residues 2-116
KeywordsIMMUNE SYSTEM / amyloid / antibody / systemic amyloidosis / light chain
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRadamaker, L. / Fandrich, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2969 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM reveals structural breaks in a patient-derived amyloid fibril from systemic AL amyloidosis.
Authors: Lynn Radamaker / Julian Baur / Stefanie Huhn / Christian Haupt / Ute Hegenbart / Stefan Schönland / Akanksha Bansal / Matthias Schmidt / Marcus Fändrich /
Abstract: Systemic AL amyloidosis is a debilitating and potentially fatal disease that arises from the misfolding and fibrillation of immunoglobulin light chains (LCs). The disease is patient-specific with ...Systemic AL amyloidosis is a debilitating and potentially fatal disease that arises from the misfolding and fibrillation of immunoglobulin light chains (LCs). The disease is patient-specific with essentially each patient possessing a unique LC sequence. In this study, we present two ex vivo fibril structures of a λ3 LC. The fibrils were extracted from the explanted heart of a patient (FOR005) and consist of 115-residue fibril proteins, mainly from the LC variable domain. The fibril structures imply that a 180° rotation around the disulfide bond and a major unfolding step are necessary for fibrils to form. The two fibril structures show highly similar fibril protein folds, differing in only a 12-residue segment. Remarkably, the two structures do not represent separate fibril morphologies, as they can co-exist at different z-axial positions within the same fibril. Our data imply the presence of structural breaks at the interface of the two structural forms.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
D: lambda 3 immunoglobulin light chain fragment, residues 2-116
E: lambda 3 immunoglobulin light chain fragment, residues 2-116
F: lambda 3 immunoglobulin light chain fragment, residues 2-116
C: lambda 3 immunoglobulin light chain fragment, residues 2-116
B: lambda 3 immunoglobulin light chain fragment, residues 2-116
A: lambda 3 immunoglobulin light chain fragment, residues 2-116


Theoretical massNumber of molelcules
Total (without water)56,5886
Polymers56,5886
Non-polymers00
Water0
1


  • Idetical with deposited unit
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  • Evidence: mass spectrometry, identification of the light chain fragment constructing the fibril
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area36600 Å2
ΔGint-108 kcal/mol
Surface area19350 Å2
MethodPISA

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Components

#1: Protein
lambda 3 immunoglobulin light chain fragment, residues 2-116


Mass: 9431.303 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: Heart / Tissue: heart muscle

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Amyloid fibril of an antibody lambda 3 immunoglobulin light chain
Type: COMPLEX
Details: Extracted fibrils from the explanted heart of a systemic AL amyloidosis patient
Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Organ: Heart / Tissue: Heart muscle
Buffer solutionpH: 7
Buffer componentName: Distilled water / Formula: H2O
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample in pure water, pH not determined
Specimen supportDetails: 40 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K / Details: blot for 9s before plunging

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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 / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1964
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40

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Processing

EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4Gctf1.06CTF correction
7Coot0.8.9.2model fittingBackbone was traced using baton mode; backbone mutated to the protein sequence; real-space refinement with restraints
9PHENIX1.16model refinementphenix.real_space_refine
13RELION2.1.03D reconstruction
Image processingDetails: Motion-corrected and dose-weighted movie frames
CTF correctionDetails: CTF was estimated from the non-dose-weighted micrographs
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.1 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 194502
Details: manual particle picking helical start-end coordinates
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11003 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingB value: 73.24 / Protocol: OTHER / Space: REAL
Target criteria: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Details: Secondary structure restraints and NCS were applied during refinement

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