Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bacterial respiratory cytochrome bc1-cbb3 supercomplex

ABSTRACT: Cryo-EM Structures of Respiratory bc1-cbb3 type CIII2CIV Supercomplex and Electronic Communication Between the Complexes

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Rhodobacter Capsulatus

SUBMITTER: Hee Jong Kim

LAB HEAD: benjamin aaron garcia

PROVIDER: PXD020038 | Pride | 2021-03-23

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20190406-hjk-stefan-peak1x2-6mM-DSBU-A10.raw	Raw
	20190406-hjk-stefan-peak1x2-6mM-DSBU-A11.raw	Raw
	20190406-hjk-stefan-peak1x2-6mM-DSBU-A12.raw	Raw
	20190406-hjk-stefan-peak1x2-6mM-DSBU-B1.raw	Raw
	20190426-hjk-3-dsbu-stefan-peak2-rt205min-inj3ul.raw	Raw

Items per page:

1 - 5 of 75

Publications

Cryo-EM structures of engineered active bc1-cbb3 type CIII2CIV super-complexes and electronic communication between the complexes.

Steimle Stefan S van Eeuwen Trevor T Ozturk Yavuz Y Kim Hee Jong HJ Braitbard Merav M Selamoglu Nur N Garcia Benjamin A BA Schneidman-Duhovny Dina D Murakami Kenji K Daldal Fevzi F

Nature communications 20210210 1

Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc1 (Complex III, CIII2), and may have specific cbb3-type cyt c oxidases (Complex IV, CIV) instead of the canonical aa3-type CIV. Electron transfer between these complexes is mediated by soluble (c2) and membrane-anchored (cy) cyts. Here, we repo ...[more]

PMID: 33568648

Similar Datasets

Phomopsis amygdala fusicoccadiene synthase

Project description:Fusicoccadiene synthase from Phomopsis amygdali (PaFS) catalyzes the first committed step in the biosynthesis of Fusicoccin A, a diterpene glycoside and a a potential therapeutic agent. PaFS contains a C-terminal prenyltransferase domain that generates geranylgeranyl diphosphate (GGPP) and an N-terminal cyclase domain that utilizes GGPP to generate fusicoccadiene, which comprises the complex 5-8-5 tricyclic hydrocarbon skeleton of Fusicoccin A. The C-termimal domain octamerizes to form a central core, with the eight cyclase domains radiating outward via flexible linker segments with variable extended conformations. Crosslinking-mass spectrometry (XL-MS) experiments affirm and reveal inter-domain interactions, showing that compact conformations can be achieved. These studies, complemented by cryo-EM and functional studies, provide a framework for understanding substrate channeling between consecutive catalytic domains.

2021-07-07 | PXD021007 | Pride

Cryo-EM Structure of the bcc-aa3 respiratory chain supercomplex from Corynebacterium glutamicum

Project description:Cryo-EM Structure of the bcc-aa3 respiratory chain supercomplex from Corynebacterium glutamicum

2019-05-29 | MSV000083873 | MassIVE

HPLC-TIMS-TOF-MS of purified mitochondrial I+III2 supercomplex from Arabidopsis thaliana

Project description:Mitochondrial I+III2 supercomplex was purified from Arabidopsis thaliana cells using differential centrifugation including Percoll step gradients and continuous sucrose gradients. Supercomplex fractions were digested with trypsin using the SP3 approach. Peptides were further purified with SepPak cartridges and measured by HPLC-ESI-TIMS-TOF-MS. Database search was performed with MaxQuant (Version 2.0.3.0.) Over 1,300 proteins were identified using this highly sensitive approach, including all known subunits of the I+III2 supercomplex. This MS analysis is part of a publication on the structure of the I+III2 supercomplex from Arabidopsis by Klusch et al., 2022.

2022-12-30 | PXD036482 | Pride

VCF1 is a p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates

Project description:The hexameric AAA+ ATPase p97/VCP functions as an essential mediator of ubiquitin-dependent cellular processes, extracting ubiquitylated proteins from macromolecular complexes or membranes by catalyzing their unfolding. p97 is directed to ubiquitylated client proteins via multiple cofactors, most of which interact with the p97 N-domain. Here, we discover that FAM104A, a protein of unknown function also named VCF1 (VCP/p97 nuclear Cofactor Family member 1), acts as a novel p97 cofactor in human cells. Detailed structure-function studies reveal that VCF1 directly binds p97 via a conserved novel -helical motif that recognizes the p97 N-domain with unusually high affinity, exceeding that of other cofactors. We show that VCF1 engages in joint p97 complex formation with the heterodimeric primary p97 cofactor UFD1-NPL4 and promotes p97-UFD1-NPL4-dependent proteasomal degradation of ubiquitylated substrates in cells. Mechanistically, VCF1 indirectly stimulates UFD1-NPL4 interactions with ubiquitin conjugates via its binding to p97 but has no intrinsic affinity for ubiquitin. Collectively, our findings establish VCF1 as an unconventional p97 cofactor that promotes p97-dependent protein turnover by facilitating p97-UFD1-NPL4 recruitment to ubiquitylated targets.

2024-03-14 | PXD043563 | Pride

Supercomplex-associated Cox26 protein binds to cytochrome c oxidase.

Project description:Here we identified a hydrophobic 6.4kDa protein, Cox26, as a novel component of yeast mitochondrial supercomplex comprising respiratory complexes III and IV. Multi-dimensional native and denaturing electrophoretic techniques were used to identify proteins interacting with Cox26. The majority of the Cox26 protein was found non-covalently bound to the complex IV moiety of the III-IV supercomplexes. A population of Cox26 was observed to exist in a disulfide bond partnership with the Cox2 subunit of complex IV. No pronounced growth phenotype for Cox26 deficiency was observed, indicating that Cox26 may not play a critical role in the COX enzymology, and we speculate that Cox26 may serve to regulate or support the Cox2 protein. Respiratory supercomplexes are assembled in the absence of the Cox26 protein, however their pattern slightly differs to the wild type III-IV supercomplex appearance. The catalytic activities of complexes III and IV were observed to be normal and respiration was comparable to wild type as long as cells were cultivated under normal growth conditions. Stress conditions, such as elevated temperatures resulted in mild decrease of respiration in non-fermentative media when the Cox26 protein was absent.

| S-EPMC7140176 | biostudies-literature

Atomic structures of respiratory complex III2 complex IV and supercomplex III2-IV from vascular plants

Project description:Mitochondrial complex III (CIII2) and complex IV (CIV) which can associate into a higher-order supercomplex (SC III2 IV) play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII2, CIV and SC III2 IV from Vigna radiata determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII2 and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII2 revealed long-range, coordinated movements across the complex as well as the motion of CIII2s iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H-channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes, generate new mechanistic hypotheses and allow for the generation of more selective agricultural inhibitors.

2020-10-05 | MSV000086237 | MassIVE

Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc1.

Project description:Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is found solely in an SC with cytochrome bc1 (complex III, CIII). Here, we present the cryogenic electron microscopy (cryo-EM) structure of S. cerevisiae CIV in a III2IV2 SC at 3.3 Å resolution. While overall similarity to mammalian homologs is high, we found notable differences in the supernumerary subunits Cox26 and Cox13; the latter exhibits a unique arrangement that precludes CIV dimerization as seen in bovine. A conformational shift in the matrix domain of Cox5A-involved in allosteric inhibition by ATP-may arise from its association with CIII. The CIII-CIV arrangement highlights a conserved interaction interface of CIII, albeit one occupied by complex I in mammalian respirasomes. We discuss our findings in the context of the potential impact of SC formation on CIV regulation.

| S-EPMC6330080 | biostudies-literature

Respiratory supercomplexes provide metabolic efficiency in zebrafish

Project description:The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 (cox7a2l) is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III-IV complexes. Therefore the SCAF1 null allele model lack all III-IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources.

2020-05-03 | GSE133487 | GEO

Cryo-EM structure and kinetics reveal electron transfer by 2D diffusion of cytochrome c in the yeast III-IV respiratory supercomplex.

Project description:Energy conversion in aerobic organisms involves an electron current from low-potential donors, such as NADH and succinate, to dioxygen through the membrane-bound respiratory chain. Electron transfer is coupled to transmembrane proton transport, which maintains the electrochemical proton gradient used to produce ATP and drive other cellular processes. Electrons are transferred from respiratory complexes III to IV (CIII and CIV) by water-soluble cytochrome (cyt.) c In Saccharomyces cerevisiae and some other organisms, these complexes assemble into larger CIII2CIV1/2 supercomplexes, the functional significance of which has remained enigmatic. In this work, we measured the kinetics of the S. cerevisiae supercomplex cyt. c-mediated QH2:O2 oxidoreductase activity under various conditions. The data indicate that the electronic link between CIII and CIV is confined to the surface of the supercomplex. Single-particle electron cryomicroscopy (cryo-EM) structures of the supercomplex with cyt. c show the positively charged cyt. c bound to either CIII or CIV or along a continuum of intermediate positions. Collectively, the structural and kinetic data indicate that cyt. c travels along a negatively charged patch on the supercomplex surface. Thus, rather than enhancing electron transfer rates by decreasing the distance that cyt. c must diffuse in three dimensions, formation of the CIII2CIV1/2 supercomplex facilitates electron transfer by two-dimensional (2D) diffusion of cyt. c This mechanism enables the CIII2CIV1/2 supercomplex to increase QH2:O2 oxidoreductase activity and suggests a possible regulatory role for supercomplex formation in the respiratory chain.

| S-EPMC7980474 | biostudies-literature

Identification of a protein mediating respiratory supercomplex stability.

Project description:The complexes of the electron transport chain associate into large macromolecular assemblies, which are believed to facilitate efficient electron flow. We have identified a conserved mitochondrial protein, named respiratory supercomplex factor 1 (Rcf1-Yml030w), that is required for the normal assembly of respiratory supercomplexes. We demonstrate that Rcf1 stably and independently associates with both Complex III and Complex IV of the electron transport chain. Deletion of the RCF1 gene caused impaired respiration, probably as a result of destabilization of respiratory supercomplexes. Consistent with the hypothetical function of these respiratory assemblies, loss of RCF1 caused elevated mitochondrial oxidative stress and damage. Finally, we show that knockdown of HIG2A, a mammalian homolog of RCF1, causes impaired supercomplex formation. We suggest that Rcf1 is a member of an evolutionarily conserved protein family that acts to promote respiratory supercomplex assembly and activity.

| S-EPMC3302151 | biostudies-literature