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Yorodumi- PDB-8s5l: Full-length human cystathionine beta-synthase, basal state, parti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8s5l | ||||||
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Title | Full-length human cystathionine beta-synthase, basal state, partially degraded tetramer | ||||||
Components | (Cystathionine beta-synthaseCystathionine beta synthase) x 2 | ||||||
Keywords | TRANSFERASE / Filament / Allostery | ||||||
Function / homology | Function and homology information Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / L-serine catabolic process / carbon monoxide binding ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / L-serine catabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process / cartilage development involved in endochondral bone morphogenesis / L-serine metabolic process / regulation of nitric oxide mediated signal transduction / L-cysteine catabolic process / cysteine biosynthetic process / cerebellum morphogenesis / nitric oxide binding / cysteine biosynthetic process from serine / DNA protection / endochondral ossification / transsulfuration / S-adenosyl-L-methionine binding / response to folic acid / nitrite reductase (NO-forming) activity / superoxide metabolic process / maternal process involved in female pregnancy / blood vessel remodeling / blood vessel diameter maintenance / oxygen binding / pyridoxal phosphate binding / cellular response to hypoxia / ubiquitin protein ligase binding / heme binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / identical protein binding / 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 | McCorvie, T.J. / Yue, W.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Architecture and regulation of filamentous human cystathionine beta-synthase. Authors: Thomas J McCorvie / Douglas Adamoski / Raquel A C Machado / Jiazhi Tang / Henry J Bailey / Douglas S M Ferreira / Claire Strain-Damerell / Arnaud Baslé / Andre L B Ambrosio / Sandra M G Dias / Wyatt W Yue / Abstract: Cystathionine beta-synthase (CBS) is an essential metabolic enzyme across all domains of life for the production of glutathione, cysteine, and hydrogen sulfide. Appended to the conserved catalytic ...Cystathionine beta-synthase (CBS) is an essential metabolic enzyme across all domains of life for the production of glutathione, cysteine, and hydrogen sulfide. Appended to the conserved catalytic domain of human CBS is a regulatory domain that modulates activity by S-adenosyl-L-methionine (SAM) and promotes oligomerisation. Here we show using cryo-electron microscopy that full-length human CBS in the basal and SAM-bound activated states polymerises as filaments mediated by a conserved regulatory domain loop. In the basal state, CBS regulatory domains sterically block the catalytic domain active site, resulting in a low-activity filament with three CBS dimers per turn. This steric block is removed when in the activated state, one SAM molecule binds to the regulatory domain, forming a high-activity filament with two CBS dimers per turn. These large conformational changes result in a central filament of SAM-stabilised regulatory domains at the core, decorated with highly flexible catalytic domains. Polymerisation stabilises CBS and reduces thermal denaturation. In PC-3 cells, we observed nutrient-responsive CBS filamentation that disassembles when methionine is depleted and reversed in the presence of SAM. Together our findings extend our understanding of CBS enzyme regulation, and open new avenues for investigating the pathogenic mechanism and therapeutic opportunities for CBS-associated disorders. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s5l.cif.gz | 573 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s5l.ent.gz | 476.9 KB | Display | PDB format |
PDBx/mmJSON format | 8s5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/8s5l ftp://data.pdbj.org/pub/pdb/validation_reports/s5/8s5l | HTTPS FTP |
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-Related structure data
Related structure data | 19739MC 8s5hC 8s5iC 8s5jC 8s5kC 8s5mC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 60980.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Production host: Escherichia coli (E. coli) / References: UniProt: P35520, cystathionine beta-synthase #2: Protein | Mass: 60752.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Production host: Escherichia coli (E. coli) / References: UniProt: P35520, cystathionine beta-synthase #3: Chemical | ChemComp-HEM / #4: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Helical assembly of full-length human cystathionine beta-synthase in the basal state Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: filter sterile 25 mM HEPES, pH 7.5, 200 mM NaCl, 2.0 mM TCEP, 0.005% (v/v) tween-20 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 150000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1400 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5.18 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2628 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1190611 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67901 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 64.75 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4COO Accession code: 4COO / Source name: PDB / Type: experimental model |