Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data

Lasker, Keren; Phillips, Jeremy; Russel, Daniel; Velázquez-Muriel, Javier; Stroopinsky, Dina; Tjioe, Elina; Webb, Ben; Schlessinger, Avner; Šali, Andrej

doi:10.1074/mcp.r110.000067

Cited by 66 publications

(65 citation statements)

References 146 publications

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“…The confidence in the accuracy of the ensemble is based on three considerations (27,31). First, the ensemble models satisfy most of the independently determined data points.…”

Section: Stage 2: System Representation and Translation Of Informatiomentioning

confidence: 99%

“…As a consequence, X-ray crystallographic analysis of the entire RP has not yet been accomplished, although the atomic structures of a few subunit fragments have been determined (9,(24)(25)(26). To overcome limitations in sample preparation and individual structure-determination techniques, we have applied an integrative structure determination approach in which a variety of different datasets were computationally integrated into a more accurate and higher-resolution structural model than is possible with any of the individual datasets (27)(28)(29). In particular, we have determined the structure of the complete 26S proteasome from Schizosaccharomyces pombe, based on a new 8.4-Å cryo-EM map, residue-specific intersubunit cross-links, crystallographic structures of RP subunit homologs, as well as previously published protein-protein interaction data from a variety of species.…”

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confidence: 99%

“…To determine the positions, orientations, and conformations of the Rpn subunits and the AAA-ATPase hexamer, we applied an integrative approach implemented in our open source Integrative Modeling Platform (IMP) package (http://salilab.org/imp/) (27,28,31). The process consists of four stages: gathering information about the structure of the 26S proteasome, choosing how to represent the system and how to translate the information into spatial restraints, calculating an ensemble of structures that satisfy these restraints, and analyzing the ensemble (Fig.…”

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confidence: 99%

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Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

Lasker

Förster

Bohn

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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The 26S proteasome is at the executive end of the ubiquitinproteasome pathway for the controlled degradation of intracellular proteins. While the structure of its 20S core particle (CP) has been determined by X-ray crystallography, the structure of the 19S regulatory particle (RP), which recruits substrates, unfolds them, and translocates them to the CP for degradation, has remained elusive. Here, we describe the molecular architecture of the 26S holocomplex determined by an integrative approach based on data from cryoelectron microscopy, X-ray crystallography, residue-specific chemical cross-linking, and several proteomics techniques. The "lid" of the RP (consisting of Rpn3/5/6/7/8/9/11/12) is organized in a modular fashion. Rpn3/5/6/7/9/12 form a horseshoe-shaped heterohexamer, which connects to the CP and roofs the AAAATPase module, positioning the Rpn8/Rpn11 heterodimer close to its mouth. Rpn2 is rigid, supporting the lid, while Rpn1 is conformationally variable, positioned at the periphery of the ATPase ring. The ubiquitin receptors Rpn10 and Rpn13 are located in the distal part of the RP, indicating that they were recruited to the complex late in its evolution. The modular structure of the 26S proteasome provides insights into the sequence of events prior to the degradation of ubiquitylated substrates.coiled coils | mass spectrometry | proteasome-COP9-eIF3 domain | proteasome-cyclosome repeats I n eukaryotes, the ubiquitin-proteasome pathway (UPP) is essential for proteostasis: Misfolded proteins or otherwise defective proteins as well as short-lived regulatory proteins are eliminated by degradation (1). The UPP regulates many fundamental cellular processes, such as protein quality control, DNA repair, and signal transduction (for review see ref.2). The 26S proteasome is the most downstream element of the UPP, executing the degradation of polyubiquitylated substrates (3-5). It consists of the barrelshaped core particle (CP; approximately 700 kDa), which sequesters the proteolytically active site in its central cavity, and the regulatory particle (RP; approximately 900 kDa), which is attached at either one or both ends of the CP and prepares substrates for degradation (6).The RP consists of 19 different canonical subunits, including six regulatory particle AAA-ATPase subunits (Rpt1-6) and 13 regulatory particle non-ATPase subunits (Rpn1-3, Rpn5-13, and Rpn15). The integral ubiquitin (Ub) receptors Rpn10 and Rpn13 recognize polyubiquitylated substrates (7-9). Alternatively, polyubiquitylated substrates can be recruited by shuttling Ub-receptors (Dsk2, Rad23, Ddi2), which bind to substrates with their Ub-associated domain, and to Rpn1, Rpn10, or Rpn13 at their Ub-like domain (5). The metalloprotease Rpn11 deubiquitylates substrates prior to their degradation (10, 11). The functions of the other Rpn subunits remain to be established. The AAA-ATPases form a hexameric ring that unfolds substrates, opens the gate to the CP, and eventually translocates the substrates to the CP.Electron microscopy (EM) (12) and X-...

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“…The confidence in the accuracy of the ensemble is based on three considerations (27,31). First, the ensemble models satisfy most of the independently determined data points.…”

Section: Stage 2: System Representation and Translation Of Informatiomentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

Lasker

Förster

Bohn

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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426

513

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“…Finally, we reviewed how different sources of experimental data are synergistically used to model large macromolecular complexes by the Integrative Modelling Platform (Lasker et al, 2010a). This approach has successfully been used to elucidate the structure of the nucleopore complex or the structure of chromatin at megabase scale.…”

Section: Discussionmentioning

confidence: 99%

“…In this way, Sali and collaborators developed an integrative modeling platform (IMP) (Lasker et al, 2010a) that collect this information and consider them simultaneously to generate models consistent with the data. This platform was used to describe the nuclear pore complex (Alber et al, 2007) and the structure of chromatin at megabase scale (Bau et al, 2010).…”

Section: Integrative Modelingmentioning

confidence: 99%

Structural Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from Sequence

Oliva¹,

Planas-Iglesias²,

Bonet³

et al. 2012

Protein-Protein Interactions - Computational and Experimental Tools

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Computational Protein–Protein Docking

Zacharias

2022

Protein Interactions

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Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data

Cited by 66 publications

References 146 publications

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

Structural Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from Sequence

Computational Protein–Protein Docking

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