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SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM
SPHIRE-crYOLO is presented, a particle picking software for selecting particles from digital micrographs in cryoEM data that automatically recognizes particles with high recall and precision, simplifying data pre-processing.
Copper-transporting P-type ATPases use a unique ion-release pathway
It is shown by molecular dynamics simulations that extracellular water solvated the transmembrane (TM) domain, results indicative of a Cu+-release pathway, and a new LpCopA crystal structure determined at 2-Å resolution delineated the same passage, and site-directed-mutagenesis activity assays support a functional role for the conduit.
SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM.
The particle picking software crYOLO which is based on the deep-learning object detection system You Only Look Once (YO) is presented, allowing for completely automated on-the-fly cryo-EM data preprocessing during data acquisition.
Structure and mechanism of Zn2+-transporting P-type ATPases
The findings suggest a mechanistic link between PIB-type Zn2+-ATPases and PIII-type H+-ATORases and at the same time show structural features of the extracellular release pathway that resemble PII-type ATPases such as the sarcoplasmic/endoplasmsic reticulum Ca2-atPase (SERCA) and Na+, K+- ATPase.
Structural models of the human copper P-type ATPases ATP7A and ATP7B
Homology models based on the existing structures of soluble domains and the recently determined structure of the homologous LpCopA from the bacterium Legionella pneumophila show that the domains and residues involved in the catalytic phosphorylation events and copper transfer are highly conserved, mimicking the single or dual HMBDs found in most copper-specific P-type ATPases.
Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams.
Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization, suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization.
Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser
The structure determination of P-type ATPase–ligand complexes from microcrystals by serial femtosecond crystallography using a free-electron laser is described. The feasibility of the method for
A sulfur‐based transport pathway in Cu+‐ATPases
Structural analysis indicates that Cu+ is bound at a high‐affinity transmembrane‐binding site in a trigonal‐planar coordination with the Cys residues of the conserved CPC motif of trans Membrane segment 4 (C382 and C384) and the Conserved Met residue of transmemBRane segment 6 (M717 of the MXXXS motif).
Structure and Function of Cu(I)- and Zn(II)-ATPases.
The Cu(I)- and Zn(II)-ATPases are compared, scrutinizing the molecular differences that allow transport of these two distinct metal types, and possible future directions of research in the field are discussed.