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- PDB-9fab: Additional cryo-EM structure of cardiac amyloid AL59 - bent polymorph -

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Basic information

Entry
Database: PDB / ID: 9fab
TitleAdditional cryo-EM structure of cardiac amyloid AL59 - bent polymorph
ComponentsMonoclonal immunoglobulin light chains (LC)
KeywordsPROTEIN FIBRIL / systemic AL amyloid fibril
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSchulte, T. / Speranzini, V. / Chaves-Sanjuan, A. / Milazzo, M. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationPRIN 2020 (20207XLJB2) Italy
CitationJournal: To be published
Title: Additional cryo-EM structure of cardiac amyloid AL59 - bent polymorph
Authors: Schulte, T. / Chaves-Sanjuan, A. / Speranzini, V. / Sicking, K. / Milazzo, M. / Mazzini, G. / Rognoni, P. / Caminito, S. / Milani, P. / Marabelli, C. / Corbelli, A. / Diomede, L. / ...Authors: Schulte, T. / Chaves-Sanjuan, A. / Speranzini, V. / Sicking, K. / Milazzo, M. / Mazzini, G. / Rognoni, P. / Caminito, S. / Milani, P. / Marabelli, C. / Corbelli, A. / Diomede, L. / Fiordaliso, F. / Anastasia, L. / Pappone, C. / Merlini, G. / Bolognesi, M. / Nuvolone, M. / Fernandez-Busnadiego, R. / Palladini, G. / Ricagno, S.
History
DepositionMay 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monoclonal immunoglobulin light chains (LC)
B: Monoclonal immunoglobulin light chains (LC)
C: Monoclonal immunoglobulin light chains (LC)
D: Monoclonal immunoglobulin light chains (LC)
E: Monoclonal immunoglobulin light chains (LC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,72310
Polymers69,6175
Non-polymers1,1065
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
Monoclonal immunoglobulin light chains (LC)


Mass: 13923.335 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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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: Monoclonal immunoglobulin light chains (LC), fibrillar form
Type: TISSUE
Details: Amyloid fibrils extracted ex vivo from cardiac tissue of AL patient
Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 magnification: 120000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2049

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.7351 ° / Axial rise/subunit: 4.9162 Å / Axial symmetry: C1
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23010 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.014515
ELECTRON MICROSCOPYf_angle_d1.576160
ELECTRON MICROSCOPYf_dihedral_angle_d11.321570
ELECTRON MICROSCOPYf_chiral_restr0.07700
ELECTRON MICROSCOPYf_plane_restr0.007795

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