+Open data
-Basic information
Entry | Database: PDB / ID: 6r8f | ||||||
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Title | Cryo-EM structure of the Human BRISC-SHMT2 complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Complex / Deubiquitylation / Ubiquitin / Immune signalling | ||||||
Function / homology | Function and homology information : / peroxisome targeting sequence binding / BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / : / BRCA1-A complex / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process ...: / peroxisome targeting sequence binding / BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / : / BRCA1-A complex / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / attachment of spindle microtubules to kinetochore / L-serine metabolic process / nuclear ubiquitin ligase complex / glycine metabolic process / L-serine biosynthetic process / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / regulation of DNA damage checkpoint / regulation of oxidative phosphorylation / Metabolism of folate and pterines / metal-dependent deubiquitinase activity / tetrahydrofolate metabolic process / response to type I interferon / tumor necrosis factor receptor binding / mitotic G2/M transition checkpoint / protein K63-linked deubiquitination / tetrahydrofolate interconversion / K63-linked deubiquitinase activity / regulation of aerobic respiration / response to ionizing radiation / folic acid metabolic process / mitochondrial nucleoid / protein deubiquitination / mitotic G2 DNA damage checkpoint signaling / mitotic spindle assembly / polyubiquitin modification-dependent protein binding / RHOG GTPase cycle / response to X-ray / regulation of DNA repair / enzyme regulator activity / protein autoubiquitination / ubiquitin ligase complex / positive regulation of DNA repair / mRNA regulatory element binding translation repressor activity / response to ischemia / chromosome segregation / cellular response to ionizing radiation / protein tetramerization / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Metalloprotease DUBs / mRNA 5'-UTR binding / spindle pole / metallopeptidase activity / microtubule cytoskeleton / double-strand break repair / pyridoxal phosphate binding / one-carbon metabolic process / mitotic cell cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / Processing of DNA double-strand break ends / protein homotetramerization / microtubule binding / mitochondrial inner membrane / cysteine-type deubiquitinase activity / microtubule / mitochondrial matrix / cell division / apoptotic process / DNA damage response / chromatin binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / signal transduction / protein homodimerization activity / mitochondrion / extracellular exosome / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Walden, M. / Hesketh, E. / Tian, L. / Ranson, N.A. / Greenberg, R.A. / Zeqiraj, E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nature / Year: 2019 Title: Metabolic control of BRISC-SHMT2 assembly regulates immune signalling. Authors: Miriam Walden / Lei Tian / Rebecca L Ross / Upasana M Sykora / Dominic P Byrne / Emma L Hesketh / Safi K Masandi / Joel Cassel / Rachel George / James R Ault / Farid El Oualid / Krzysztof ...Authors: Miriam Walden / Lei Tian / Rebecca L Ross / Upasana M Sykora / Dominic P Byrne / Emma L Hesketh / Safi K Masandi / Joel Cassel / Rachel George / James R Ault / Farid El Oualid / Krzysztof Pawłowski / Joseph M Salvino / Patrick A Eyers / Neil A Ranson / Francesco Del Galdo / Roger A Greenberg / Elton Zeqiraj / Abstract: Serine hydroxymethyltransferase 2 (SHMT2) regulates one-carbon transfer reactions that are essential for amino acid and nucleotide metabolism, and uses pyridoxal-5'-phosphate (PLP) as a cofactor. ...Serine hydroxymethyltransferase 2 (SHMT2) regulates one-carbon transfer reactions that are essential for amino acid and nucleotide metabolism, and uses pyridoxal-5'-phosphate (PLP) as a cofactor. Apo SHMT2 exists as a dimer with unknown functions, whereas PLP binding stabilizes the active tetrameric state. SHMT2 also promotes inflammatory cytokine signalling by interacting with the deubiquitylating BRCC36 isopeptidase complex (BRISC), although it is unclear whether this function relates to metabolism. Here we present the cryo-electron microscopy structure of the human BRISC-SHMT2 complex at a resolution of 3.8 Å. BRISC is a U-shaped dimer of four subunits, and SHMT2 sterically blocks the BRCC36 active site and inhibits deubiquitylase activity. Only the inactive SHMT2 dimer-and not the active PLP-bound tetramer-binds and inhibits BRISC. Mutations in BRISC that disrupt SHMT2 binding impair type I interferon signalling in response to inflammatory stimuli. Intracellular levels of PLP regulate the interaction between BRISC and SHMT2, as well as inflammatory cytokine responses. These data reveal a mechanism in which metabolites regulate deubiquitylase activity and inflammatory signalling. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6r8f.cif.gz | 364 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r8f.ent.gz | 295 KB | Display | PDB format |
PDBx/mmJSON format | 6r8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/6r8f ftp://data.pdbj.org/pub/pdb/validation_reports/r8/6r8f | HTTPS FTP |
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-Related structure data
Related structure data | 4759MC 4760C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 36119.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRCC3, BRCC36, C6.1A, CXorf53 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P46736, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases #2: Protein | Mass: 31033.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABRAXAS2, ABRO1, FAM175B, KIAA0157 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15018 #3: Protein | Mass: 56097.902 Da / Num. of mol.: 2 / Mutation: A285T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Production host: Escherichia coli (E. coli) References: UniProt: P34897, glycine hydroxymethyltransferase #4: Protein | Mass: 22026.717 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BABAM2, BRCC45, BRE, BABAM2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NXR7 #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 388.47 kDa/nm / Experimental value: YES | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.051 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Specimen contained BRCC36, ABRAXAS2, BRCC45, MERIT40 and SHMT2 macromolecules | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: -1600 nm / Nominal defocus min: -3100 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 1.2 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 7494 |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 403499 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||
Atomic model building |
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