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- PDB-8cpe: CryoEM structure of AL55 amyloid fibrils extracted from the kidne... -

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Basic information

Entry
Database: PDB / ID: 8cpe
TitleCryoEM structure of AL55 amyloid fibrils extracted from the kidney of an AL amyloidosis patient.
ComponentsImmunoglobulin lambda light chain
KeywordsPROTEIN FIBRIL / Light chains / Amyloid fibrils / AL amyloidosis.
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å
AuthorsPuri, S. / Schulte, T. / Chaves-Sanjuan, A. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other government20207XLJB2 Italy
CitationJournal: J Mol Biol / Year: 2023
Title: The Cryo-EM STRUCTURE of Renal Amyloid Fibril Suggests Structurally Homogeneous Multiorgan Aggregation in AL Amyloidosis.
Authors: Sarita Puri / Tim Schulte / Antonio Chaves-Sanjuan / Giulia Mazzini / Serena Caminito / Carlo Pappone / Luigi Anastasia / Paolo Milani / Giampaolo Merlini / Martino Bolognesi / Mario ...Authors: Sarita Puri / Tim Schulte / Antonio Chaves-Sanjuan / Giulia Mazzini / Serena Caminito / Carlo Pappone / Luigi Anastasia / Paolo Milani / Giampaolo Merlini / Martino Bolognesi / Mario Nuvolone / Giovanni Palladini / Stefano Ricagno /
Abstract: Immunoglobulin light chain amyloidosis (AL) is caused by the aberrant production of amyloidogenic light chains (LC) that accumulate as amyloid deposits in vital organs. Distinct LC sequences in each ...Immunoglobulin light chain amyloidosis (AL) is caused by the aberrant production of amyloidogenic light chains (LC) that accumulate as amyloid deposits in vital organs. Distinct LC sequences in each patient yield distinct amyloid structures. However different tissue microenvironments may also cause identical protein precursors to adopt distinct amyloid structures. To address the impact of the tissue environment on the structural polymorphism of amyloids, we extracted fibrils from the kidney of an AL patient (AL55) whose cardiac amyloid structure was previously determined by our group. Here we show that the 4.0 Å resolution cryo-EM structure of the renal fibril is virtually identical to that reported for the cardiac fibril. These results provide the first structural evidence that LC amyloids independently deposited in different organs of the same AL patient share a common fold.
History
DepositionMar 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Immunoglobulin lambda light chain
A: Immunoglobulin lambda light chain
B: Immunoglobulin lambda light chain
D: Immunoglobulin lambda light chain
E: Immunoglobulin lambda light chain


Theoretical massNumber of molelcules
Total (without water)116,6335
Polymers116,6335
Non-polymers00
Water00
1


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

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Components

#1: Antibody
Immunoglobulin lambda light chain


Mass: 23326.557 Da / Num. of mol.: 5 / Mutation: No / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: Kidney

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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: Renal AL55 amyloid fibrils / Type: COMPLEX
Details: Light chain amyloid fibrils named AL55 extracted from the kidney of an AL amyloidosis patient
Entity ID: all / Source: NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1819

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.1particle selection
4CTFFIND4.1CTF correction
7UCSF ChimeraXmodel fitting
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmerty
IDImage processing-IDAngular rotation/subunit (°)Axial rise/subunit (Å)Axial symmetry
11-1.634.9C1
21-1.634.9C1
Particle selectionNum. of particles selected: 98829
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49091 / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 6HUD

6hud


Accession code: 6HUD / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0022975
ELECTRON MICROSCOPYf_angle_d0.9324040
ELECTRON MICROSCOPYf_dihedral_angle_d12.165990
ELECTRON MICROSCOPYf_chiral_restr0.059435
ELECTRON MICROSCOPYf_plane_restr0.005515

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