Emdatabank: Unified Data Resource for 3DEM

Abstract

We have previously used cryo-electron tomography combined with missingwedge corrected, sub-volume averaging and classification to obtain 3D structures of macromolecular assemblies in cases where a single dominant species was present, and applied these methods to the analysis of a variety of trimeric HIV-1 and SIV envelope glycoproteins (Env). Here, we extend these studies by presenting a method for determining the distribution of conformational states found in a specimen and validate these procedures by successfully separating and reconstructing distinct 3D structures for unliganded and antibody-liganded as well as open and closed conformations of Env present simultaneously in mixtures. We show that identifying and removing spikes with the lowest signal-to-noise ratios improves the overall accuracy of alignment between individual Env sub-volumes, and that alignment accuracy, in turn, determines the success of image classification in assessing conformational heterogeneity in heterogeneous mixtures. This development extends the subtomogram averaging capabilities to heterogeneous samples. Furthermore, it turns cryo-electron tomography into a powerful analytical tool that can directly determine the relative amount of the different conformations found in the specimen.

The structure and oxidation of the eye lens chaperone αA-crystallin

“…For resolution determination, the 'gold standard' 0.143 criterion was used 77 . FSCs were calculated between the final reconstructions of independently processed half sets using the FSC validation server (http://pdbe.org/fsc) within the PDBe (Protein Data Bank in Europe) 78 . 3D reconstructions and atomic models were rendered using UCSF Chimera 79 .…”

Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis

“…All raw movie frames, micrographs, the particle stack and relevant metadata files has been deposited into EMPIAR 72 as EMPIAR-10420. The electron density map has been deposited into EMDB 73 as EMD-21983. The model has been deposited into PDB 74 as 6X0O [https://doi.org/10.2210/pdb6X0O/pdb].…”

Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes

“…Data and Model Depositions SAXS profiles, P(r) distributions, fits and models have been deposited with the Small Angle Scattering Biological Data Bank (Valentini et al, 2015) under the accession codes SASBDB: SASDEV9 (Cytohesin-2; ARF nucleotide-binding site opener, ARNO truncation mutant), SASBDB: SASDEW9 (Cytohesin-2; ARF nucleotide-binding site opener, ARNO), SASBDB: SASDG64 (Grp1 14-399 + IP4 SAXS with DAMMIF and GASBOR models), SASBDB: SASDG94 (Grp1 14-399 + IP4 SAXS with antiparallel CORAL and MultiFoXS models), SASBDB: SASDGA4 (Grp1 14-399 + IP4 SAXS with parallel CORAL and MultiFoXS models), SASBDB: SASDG74 (Grp1 14-390 + IP4 SAXS with DAMMIF and GASBOR models), SASBDB: SASDGB4 (Grp1 14-390 + IP4 SAXS with antiparallel CORAL and Multi-FoXS models), SASBDB: SASDGC4 (Grp1 14-390 + IP4 SAXS with parallel CORAL and MultiFoXS models), SASBDB: SASDG84 (ARNO 2-400 + IP4 SAXS with DAMMIF, GASBOR and antiparallel CORAL models). EM envelopes have been deposited with the EM Data Bank (Lawson et al, 2016) under the accession codes EMDB: EMD-20628 (Grp1 14-399 + IP4 NS-EM Volume 1 with best antiparallel model) and EMDB: EMD-20629 (Grp1 14-399 + IP4 NS-EM Volume 2 with best antiparallel model). The best-fitting MultiFoXS models selected by ADP_EM have been deposited with the Protein Data Bank (Berman et al, 2000) under the accession codes PDB: 6U3E (Grp1 14-399 + IP4 NS-EM Volume 1 with best antiparallel model) and PDB: 6U3G (Grp1 14-399 + IP4 NS-EM Volume 2 with best antiparallel model).…”