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TOM core complex - Cryo-EM Structure of the TOM Core Complex from Neurospora crassa

ABSTRACT: The structure of the TOM-complex from Neurospora crassa was characterized using single particle electron microscopy. In order to unambigously identify and characterize the constituting subunits and exclude the presence of previously uncharacterized subunits, the samples were analyzed using proteolytic digests and LC-MS/MS prior to EM structure determination.

INSTRUMENT(S): LTQ Orbitrap Elite, Q Exactive

ORGANISM(S): Neurospora Crassa

SUBMITTER: Julian Langer

LAB HEAD: Julian Langer

PROVIDER: PXD006827 | Pride | 2017-08-16

REPOSITORIES: Pride

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			Action	DRS
	170403_1349_ThBausewein_120min_FASP.msf	Msf
	170403_1349_ThBausewein_120min_FASP.raw	Raw
	170403_1349_ThBausewein_120min_insolution.msf	Msf
	170403_1349_ThBausewein_120min_insolution.raw	Raw

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Publications

Cryo-EM Structure of the TOM Core Complex from Neurospora crassa.

Bausewein Thomas T Mills Deryck J DJ Langer Julian D JD Nitschke Beate B Nussberger Stephan S Kühlbrandt Werner W

Cell 20170801 4

The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The complex is a 148 kDa symmetrical dimer of ten membrane protein subunits that create a shallow funnel on the cytoplasmic membrane surface. In the core of the dimer, the β-barrels of the Tom40 pore form two identical preprotein conduits. Each Tom40 pore is surrounded by the transmembrane segments of the ...[more]

PMID: 28802041

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Atomic structure of human TOM core complex.

Project description:The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for mitochondrial precursor proteins synthesized on cytosolic ribosomes. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the dimeric human TOM core complex (TOM-CC). Two Tom40 β-barrel proteins, connected by two Tom22 receptor subunits and one phospholipid, form the protein-conducting channels. The small Tom proteins Tom5, Tom6, and Tom7 surround the channel and have notable configurations. The distinct electrostatic features of the complex, including the pronounced negative interior and the positive regions at the periphery and center of the dimer on the intermembrane space (IMS) side, provide insight into the preprotein translocation mechanism. Further, two dimeric TOM complexes may associate to form tetramer in the shape of a parallelogram, offering a potential explanation into the unusual structural features of Tom subunits and a new perspective of viewing the import of mitochondrial proteins.

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Spatiotemporal stop-and-go dynamics of the mitochondrial TOM core complex correlates with channel activity.

Project description:Single-molecule studies can reveal phenomena that remain hidden in ensemble measurements. Here we show the correlation between lateral protein diffusion and channel activity of the general protein import pore of mitochondria (TOM-CC) in membranes resting on ultrathin hydrogel films. Using electrode-free optical recordings of ion flux, we find that TOM-CC switches reversibly between three states of ion permeability associated with protein diffusion. While freely diffusing TOM-CC molecules are predominantly in a high permeability state, non-mobile molecules are mostly in an intermediate or low permeability state. We explain this behavior by the mechanical binding of the two protruding Tom22 subunits to the hydrogel and a concomitant combinatorial opening and closing of the two β-barrel pores of TOM-CC. TOM-CC could thus represent a β-barrel membrane protein complex to exhibit membrane state-dependent mechanosensitive properties, mediated by its two Tom22 subunits.

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Reconstituted TOM core complex and Tim9/Tim10 complex of mitochondria are sufficient for translocation of the ADP/ATP carrier across membranes.

Project description:Precursor proteins of the solute carrier family and of channel forming Tim components are imported into mitochondria in two main steps. First, they are translocated through the TOM complex in the outer membrane, a process assisted by the Tim9/Tim10 complex. They are passed on to the TIM22 complex, which facilitates their insertion into the inner membrane. In the present study, we have analyzed the function of the Tim9/Tim10 complex in the translocation of substrates across the outer membrane of mitochondria. The purified TOM core complex was reconstituted into lipid vesicles in which purified Tim9/Tim10 complex was entrapped. The precursor of the ADP/ATP carrier (AAC) was found to be translocated across the membrane of such lipid vesicles. Thus, these components are sufficient for translocation of AAC precursor across the outer membrane. Peptide libraries covering various substrate proteins were used to identify segments that are bound by Tim9/Tim10 complex upon translocation through the TOM complex. The patterns of binding sites on the substrate proteins suggest a mechanism by which portions of membrane-spanning segments together with flanking hydrophilic segments are recognized and bound by the Tim9/Tim10 complex as they emerge from the TOM complex into the intermembrane space.

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A new twist on bacterial motility – two distinct type IV pili revealed by cryoEM

Project description:Many bacteria express filaments called type IV pili on their surface, which are involved in motility (twitching), surface adhesion, biofilm formation and DNA uptake (natural transformation). Type IV pili are comprised of a helical assembly of repeating pilin subunits that allow both flexibility and strength. They are therefore powerful structures that enable bacterial proliferation and genetic adaptation, potentially leading to the development of pathogenicity and antibiotic resistance. They are also targets for drug development. By electron cryo-microscopy and mass spectrometry, we show that the bacterium Thermus thermophilus produces two forms of type IV pilus, differing in structure and protein composition. We have determined the structures of both and built atomic models, which reveal a new pilin, how the subunits assemble and their glycosylation patterns. We also delineate the roles of the two filaments in promoting twitching and natural transformation.

2020-03-09 | PXD017353 | Pride

Non-core subunits of the PRC2 complex are collectively required for its target site specificity

Project description:The Polycomb repressive complex 2 (PRC2) catalyzes H3K27 methylation across the genome, which through involvement in transcriptional regulation is critical in establishment of cell identity. Because of its essential function during development and in cancer, understanding the establishment of genome-wide H3K27 methylation patterns has been the focus of intense investigation. PRC2 methylation activity is abundant and dispersed throughout the genome, but highest activity is specifically directed to a subset of target regions that are stably occupied by the complex and highly enriched for H3K27me3. Here we show, by systematically knocking out single and multiple non-core subunits of the PRC2 complex in mouse embryonic stem cells (mESCs), that they each contribute in directing PRC2 activity to targets sites. Furthermore, combined knockout of six non-core subunits reveal that, while dispensable for global H3K27 methylation levels, the non-core PRC2 subunits are collectively required for focusing H3K27me3 activity to specific sites in the genome.

2019-09-11 | GSE127804 | GEO

Structural insights into assembly of human mitochondrial translocase TOM complex.

Project description: Not available

| S-EPMC8041818 | biostudies-literature

Structure of nucleosome-bound human PBAF complex

Project description:BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite previous structural studies and recent advance of SWI/SNF family complexes, it remains incompletely understood how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF3-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides structural insights into PBAF-mediated nucleosome association complimentary to the recently reported PBAF-nucleosome structure.

2023-03-11 | PXD036708 | Pride

The Translin-TRAX complex/C3PO is a ribonuclease in tRNA processing

Project description:The endogenous RNA substrates of Translin-TRAX complexes (also known as C3POs) and how they regulate diverse biological processes remain unknown. Here we show that Translin and TRAX do not play a significant role in RNAi in the filamentous fungus Neurospora crassa. Instead, the Neurospora C3PO complex functions as a ribonuclease that removes the 5M-bM-^@M-^Y pre-tRNA fragments after the processing of pre-tRNAs by RNase P. In translin and trax mutants, 5M-bM-^@M-^Y pre-tRNA fragments accumulate to very high levels that can be degraded specifically by both recombinant and endogenous Neurospora C3PO and recombinant Drosophila C3PO. In addition, the mutants have elevated tRNA levels and increased levels of protein translation and are more resistant to a programmed cell-death inducing agent. Together, this study identified the endogenous RNA substrates of C3PO and provides a potential explanation for its roles in seemingly diverse biological processes. Examine small RNA population changes in two different strain background

2012-07-30 | E-GEOD-38334 | biostudies-arrayexpress

TOM complex-independent transport pathway of myoglobin into mitochondria in C2C12 myotubes.

Project description:Recently, we found that myoglobin (Mb) localizes in both the cytosol and mitochondrial intermembrane space in rodent skeletal muscle. Most proteins of the intermembrane space pass through the outer mitochondrial membrane via the translocase of the outer membrane (TOM) complex. However, whether the TOM complex imports Mb remains unknown. The purpose of this study was to investigate the involvement of the TOM complex in Mb import into the mitochondria. A proteinase K protection assay of mitochondria from C2C12 myotubes confirmed that Mb integrated into the mitochondria. An immunoprecipitation assay verified the interaction of Mb and TOM complex receptors (Tom20, Tom70) in isolated mitochondria. The assay showed a clear interaction of Mb with Tom20 and Tom70. A knockdown experiment using siRNA for TOM complex receptors (Tom20, Tom70) and TOM complex channel (Tom40) did not alter the amount of Mb expression in the mitochondrial fraction. These results suggested that Mb does not necessarily require the TOM complex for mitochondrial import of Mb. Although the physiological role of Mb interactions with TOM complex receptors remains unclear, further studies are needed to clarify how Mb enters the mitochondria independently of the TOM complex.

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Two conformations of the Tom20 preprotein receptor in the TOM holo complex.

Project description:The TOM complex is the main entry point for precursor proteins (preproteins) into mitochondria. Preproteins containing targeting sequences are recognized by the TOM complex and imported into mitochondria. We have determined the structure of the TOM core complex from Neurospora crassa by single-particle electron cryomicroscopy at 3.3 Å resolution, showing its interaction with a bound preprotein at 4 Å resolution, and of the TOM holo complex including the Tom20 receptor at 6 to 7 Å resolution. TOM is a transmembrane complex consisting of two β-barrels, three receptor subunits, and three short transmembrane subunits. Tom20 has a transmembrane helix and a receptor domain on the cytoplasmic side. We propose that Tom20 acts as a dynamic gatekeeper, guiding preproteins into the pores of the TOM complex. We analyze the interactions of Tom20 with other TOM subunits, present insights into the structure of the TOM holo complex, and suggest a translocation mechanism.

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