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

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Basic information

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
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin lambda variable 3-19
Similarity search - Component
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.
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Structure viewerMolecule:
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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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, identification of the light chain fragment constructing the fibril
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 / References: UniProt: P01714*PLUS
Has protein modificationY

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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: all / 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 FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder 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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