- EMDB-0144: Human apo-ferritin reconstructed in RELION-3.0 -
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Open data
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Basic information
Entry
Database: EMDB / ID: EMD-0144
Title
Human apo-ferritin reconstructed in RELION-3.0
Map data
Human apo-ferritin reconstructed in RELION-3.0
Sample
Complex: human apo-ferritin
Function / homology
Function and homology information
iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / iron ion binding / immune response / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function
Journal: Elife / Year: 2018 Title: New tools for automated high-resolution cryo-EM structure determination in RELION-3. Authors: Jasenko Zivanov / Takanori Nakane / Björn O Forsberg / Dari Kimanius / Wim Jh Hagen / Erik Lindahl / Sjors Hw Scheres / Abstract: Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory ...Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 Å compared to previous RELION versions.
History
Deposition
Jul 26, 2018
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Header (metadata) release
Aug 8, 2018
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Map release
Aug 8, 2018
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Update
Nov 25, 2020
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Current status
Nov 25, 2020
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
EMPIAR-10200 (Title: Human apo-ferritin reconstructed in RELION-3.0 / Data size: 191.5 Data #1: Unaligned multi-frame micrographs (in non-gain-corrected TIFF) of human apo-ferritin [micrographs - multiframe])
Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Details
Used beam shift to collect seven images within one 1.2um Quantifoil hole. Used active beamtilt compensation in TEM microscope software.
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 1255 / Average electron dose: 47.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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