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- PDB-9eme: AL amyloid fibril from the FOR103 light chain -

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Basic information

Entry
Database: PDB / ID: 9eme
TitleAL amyloid fibril from the FOR103 light chain
Componentslambda 3 immunoglobulin light chain fragment, residues 2-116
KeywordsPROTEIN FIBRIL / Amyloid fibril / AL amyloid
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsPfeiffer, P.B. / Karimi-Farsijani, S. / Kupfer, N. / Schmidt, M. / Faendrich, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2024
Title: Light chain mutations contribute to defining the fibril morphology in systemic AL amyloidosis.
Authors: Sara Karimi-Farsijani / Peter Benedikt Pfeiffer / Sambhasan Banerjee / Julian Baur / Lukas Kuhn / Niklas Kupfer / Ute Hegenbart / Stefan O Schönland / Sebastian Wiese / Christian Haupt / ...Authors: Sara Karimi-Farsijani / Peter Benedikt Pfeiffer / Sambhasan Banerjee / Julian Baur / Lukas Kuhn / Niklas Kupfer / Ute Hegenbart / Stefan O Schönland / Sebastian Wiese / Christian Haupt / Matthias Schmidt / Marcus Fändrich /
Abstract: Systemic AL amyloidosis is one of the most frequently diagnosed forms of systemic amyloidosis. It arises from mutational changes in immunoglobulin light chains. To explore whether these mutations may ...Systemic AL amyloidosis is one of the most frequently diagnosed forms of systemic amyloidosis. It arises from mutational changes in immunoglobulin light chains. To explore whether these mutations may affect the structure of the formed fibrils, we determine and compare the fibril structures from several patients with cardiac AL amyloidosis. All patients are affected by light chains that contain an IGLV3-19 gene segment, and the deposited fibrils differ by the mutations within this common germ line background. Using cryo-electron microscopy, we here find different fibril structures in each patient. These data establish that the mutations of amyloidogenic light chains contribute to defining the fibril architecture and hence the structure of the pathogenic agent.
History
DepositionMar 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,2146
Polymers73,2146
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 12202.262 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
Has protein modificationY

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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: lambda 3 immunoglobulin light chain fragment / Type: COMPLEX / Details: residues 2-116 / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7 / Details: water
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 95 %

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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 / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 10 sec. / Electron dose: 53.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2788

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Processing

EM software
IDNameVersionCategory
1RELION3.1.3particle selection
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9.2model fitting
9PHENIXmodel refinement
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 1.309 ° / Axial rise/subunit: 4.752 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 157862
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120039 / Symmetry type: HELICAL
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL / Target criteria: correlation coefficient

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