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Yorodumi- PDB-9fab: Additional cryo-EM structure of cardiac amyloid AL59 - bent polymorph -
+Open data
-Basic information
Entry | Database: PDB / ID: 9fab | ||||||
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Title | Additional cryo-EM structure of cardiac amyloid AL59 - bent polymorph | ||||||
Components | Monoclonal immunoglobulin light chains (LC) | ||||||
Keywords | PROTEIN FIBRIL / systemic AL amyloid fibril | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Schulte, T. / Speranzini, V. / Chaves-Sanjuan, A. / Milazzo, M. / Ricagno, S. | ||||||
Funding support | Italy, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9fab.cif.gz | 185.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fab.ent.gz | 152 KB | Display | PDB format |
PDBx/mmJSON format | 9fab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fab_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 9fab_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 9fab_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 9fab_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/9fab ftp://data.pdbj.org/pub/pdb/validation_reports/fa/9fab | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Antibody | Mass: 13923.335 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #2: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2049 |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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Helical symmerty | Angular rotation/subunit: -0.7351 ° / Axial rise/subunit: 4.9162 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23010 / Symmetry type: HELICAL | ||||||||||||||||||||||||
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