2024-11-13 REL PDBe PDBe PDBe 2018-12-02 2018-12-19 2019-04-03 2024-11-13 AL amyloid fibril from a lambda 1 light chain Radamaker L Schmidt M Faendrich M Fritz G amyloid fibril, beta sheet, antibody, heart, PROTEIN FIBRIL Radamaker L Lin YH Annamalai K Huhn S Hegenbart U Schonland SO Fritz G Schmidt M Fandrich M Cryo-EM structure of a light chain-derived amyloid fibril from a patient with systemic AL amyloidosis. Nat Commun UK 10 1103 1103 2019 30894526 doi:10.1038/s41467-019-09032-0 2041-1723 6ic3 FULLOVERLAP Amyloid fibril of an antibody lambda 1 light chain Amyloid fibril of an antibody lambda 1 light chain 0 1
Extracted fibrils from the heart of a patient suffering from systemic AL amyloidosis
Homo sapiens heart heart muscle 2.5 lambda 1 light chain fragment, residues 3-118 Homo sapiens Heart heart muscle 0.012177463 8 LEVO VLTQPPSASGTPGQRVTISCSGRSSNIGRNLVKWYQQFPGTAPKLLIYSNDQRPSGVPDRFSGSKSGTSASLAVSGLQSE DEADYYCAAWDATLNAWVFGGGTKLTVLSQPKAAPS helical filament 7.0 H2O distilled water C-flat-1.2/1.3 4C COPPER 400 CARBON HOLEY GLOW DISCHARGE OTHER ETHANE 80 294 GATAN CRYOPLUNGE 3
blotted from the backside for 4 s before plunging.
Sample in pure water, pH not determined
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1-30 1 847 6.0 32.0 1
Motion-corrected and dose-weighted movie frames
1 4.81 0.58 C1 FOURIER SPACE 3.3 FSC 0.143 CUT-OFF RELION 2.1.0 32677 119395
manual selection. Sigma contrast 3, lowpass filter 20 A
Initial model generation in RELION, followed by generation of a "single-fibril model" from two picked fibrils with clearly visible cross-overs
 NOT APPLICABLE emd_4452.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 333.12 333.12 333.12 90.0 90.0 90.0 X Y Z -0.042287648 0.09975388 0.0001230849 0.0020280501 1.041 1.041 1.041 0.056 AUTHOR OTHER
Refinement strategy included global minimization and local grid search and ADP were refined. Secondary structure restraints and NCS were applied during refinement.
REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) REAL 111.400000000000006