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Yorodumi- EMDB-19738: Full-length human cystathionine beta-synthase, basal state, singl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19738 | |||||||||
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Title | Full-length human cystathionine beta-synthase, basal state, single particle reconstruction | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Filament / Allostery / TRANSFERASE | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | McCorvie TJ / Yue WW | |||||||||
Funding support | United Kingdom, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19738.map.gz | 450.5 MB | EMDB map data format | |
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Header (meta data) | emd-19738-v30.xml emd-19738.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19738_fsc.xml | 16.7 KB | Display | FSC data file |
Images | emd_19738.png | 48.8 KB | ||
Masks | emd_19738_msk_1.map | 476.8 MB | Mask map | |
Filedesc metadata | emd-19738.cif.gz | 6.5 KB | ||
Others | emd_19738_additional_1.map.gz emd_19738_half_map_1.map.gz emd_19738_half_map_2.map.gz | 237.9 MB 442.8 MB 442.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19738 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19738 | HTTPS FTP |
-Related structure data
Related structure data | 8s5kMC 8s5hC 8s5iC 8s5jC 8s5lC 8s5mC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19738.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.934 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19738_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: Non-sharpened map
File | emd_19738_additional_1.map | ||||||||||||
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Annotation | Non-sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19738_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19738_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Helical assembly of full-length human cystathionine beta-synthase...
Entire | Name: Helical assembly of full-length human cystathionine beta-synthase in the basal state |
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Components |
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-Supramolecule #1: Helical assembly of full-length human cystathionine beta-synthase...
Supramolecule | Name: Helical assembly of full-length human cystathionine beta-synthase in the basal state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Cystathionine beta-synthase
Macromolecule | Name: Cystathionine beta-synthase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: cystathionine beta-synthase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 60.980578 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SMPSETPQAE VGPTGCPHRS GPHSAKGSLE KGSPEDKEAK EPLWIRPDAP SRCTWQLGRP ASESPHHHTA PAKSPKILPD ILKKIGDTP MVRINKIGKK FGLKCELLAK CEFFNAGGSV (LLP)DRISLRMIE DAERDGTLKP GDTIIEPTSG NTGIGLA LA AAVRGYRCII ...String: SMPSETPQAE VGPTGCPHRS GPHSAKGSLE KGSPEDKEAK EPLWIRPDAP SRCTWQLGRP ASESPHHHTA PAKSPKILPD ILKKIGDTP MVRINKIGKK FGLKCELLAK CEFFNAGGSV (LLP)DRISLRMIE DAERDGTLKP GDTIIEPTSG NTGIGLA LA AAVRGYRCII VMPEKMSSEK VDVLRALGAE IVRTPTNARF DSPESHVGVA WRLKNEIPNS HILDQYRNAS NPLAHYDT T ADEILQQCDG KLDMLVASVG TGGTITGIAR KLKEKCPGCR IIGVDPEGSI LAEPEELNQT EQTTYEVEGI GYDFIPTVL DRTVVDKWFK SNDEEAFTFA RMLIAQEGLL CGGSAGSTVA VAVKAAQELQ EGQRCVVILP DSVRNYMTKF LSDRWMLQKG FLKEEDLTE KKPWWWHLRV QELGLSAPLT VLPTITCGHT IEILREKGFD QAPVVDEAGV ILGMVTLGNM LSSLLAGKVQ P SDQVGKVI YKQFKQIRLT DTLGRLSHIL EMDHFALVVH EQIQYHSTGK SSQRQMVFGV VTAIDLLNFV AAQERDQK UniProtKB: Cystathionine beta-synthase |
-Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 8 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ChemComp-HEM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1.0 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: filter sterile 25 mM HEPES, pH 7.5, 200 mM NaCl, 2.0 mM TCEP, 0.005% (v/v) tween-20 | |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 150000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2628 / Average exposure time: 5.18 sec. / Average electron dose: 50.0 e/Å2 |