Protein Data Bank (PDB): the single global macromolecular structure archive

SK Burley, HM Berman, GJ Kleywegt… - … : methods and protocols, 2017 - Springer
Abstract The Protein Data Bank (PDB)––the single global repository of experimentally
determined 3D structures of biological macromolecules and their complexes––was …

Challenges and opportunities in cryo-EM single-particle analysis

D Lyumkis - Journal of Biological Chemistry, 2019 - ASBMB
Cryogenic electron microscopy (cryo-EM) enables structure determination of
macromolecular objects and their assemblies. Although the techniques have been …

EMPIAR: the electron microscopy public image archive

A Iudin, PK Korir, S Somasundharam… - Nucleic Acids …, 2023 - academic.oup.com
Public archiving in structural biology is well established with the Protein Data Bank (PDB;
wwPDB. org) catering for atomic models and the Electron Microscopy Data Bank (EMDB; …

Cryo-EM structures of SARS-CoV-2 spike without and with ACE2 reveal a pH-dependent switch to mediate endosomal positioning of receptor-binding domains

T Zhou, Y Tsybovsky, J Gorman, M Rapp, G Cerutti… - Cell host & …, 2020 - cell.com
The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the
human ACE2 receptor and to facilitate virus entry, which can occur through low-pH …

Mechanism of an intramembrane chaperone for multipass membrane proteins

L Smalinskaitė, MK Kim, AJO Lewis, RJ Keenan… - Nature, 2022 - nature.com
Multipass membrane proteins play numerous roles in biology and include receptors,
transporters, ion channels and enzymes,. How multipass proteins are co-translationally …

[PDF][PDF] Real-space refinement in PHENIX for cryo-EM and crystallography

PV Afonine, BK Poon, RJ Read… - … Section D: Structural …, 2018 - journals.iucr.org
This article describes the implementation of real-space refinement in the phenix.
real_space_refine program from the PHENIX suite. The use of a simplified refinement target …

Protein Data Bank: the single global archive for 3D macromolecular structure data

Nucleic acids research, 2019 - academic.oup.com
Abstract The Protein Data Bank (PDB) is the single global archive of experimentally
determined three-dimensional (3D) structure data of biological macromolecules. Since …

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

A Punjani, JL Rubinstein, DJ Fleet, MA Brubaker - Nature methods, 2017 - nature.com
Single-particle electron cryomicroscopy (cryo-EM) is a powerful method for determining the
structures of biological macromolecules. With automated microscopes, cryo-EM data can …

[PDF][PDF] New tools for the analysis and validation of cryo-EM maps and atomic models

PV Afonine, BP Klaholz, NW Moriarty… - … Section D: Structural …, 2018 - journals.iucr.org
Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly
increasing number of atomic models of biomacromolecules that have been solved using this …

Lysosomal LAMP proteins regulate lysosomal pH by direct inhibition of the TMEM175 channel

J Zhang, W Zeng, Y Han, WR Lee, J Liou, Y Jiang - Molecular cell, 2023 - cell.com
Maintaining a highly acidic lysosomal pH is central to cellular physiology. Here, we use
functional proteomics, single-particle cryo-EM, electrophysiology, and in vivo imaging to …