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- EMDB-19740: Full-length human cystathionine beta-synthase with C-terminal 6xH... -
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Open data
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Basic information
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Title | Full-length human cystathionine beta-synthase with C-terminal 6xHis-tag, SAM bound, activated state, helical reconstruction | |||||||||
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Function / homology | ![]() Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / ![]() | |||||||||
![]() | McCorvie TJ / Yue WW | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 8.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.2 KB 21.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.5 KB | Display | ![]() |
Images | ![]() | 63 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() ![]() | 91.6 MB 165.1 MB 165.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8s5mMC ![]() 8s5hC ![]() 8s5iC ![]() 8s5jC ![]() 8s5kC ![]() 8s5lC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Locally sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: Sharpened map
File | emd_19740_additional_1.map | ||||||||||||
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Annotation | Sharpened map | ||||||||||||
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-Half map: #1
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-Half map: #2
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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: ![]() ![]() |
-Macromolecule #1: Cystathionine beta-synthase
Macromolecule | Name: Cystathionine beta-synthase / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 61.636426 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MPSETPQAEV GPTGCPHRSG PHSAKGSLEK GSPEDKEAKE PLWIRPDAPS RCTWQLGRPA SESPHHHTAP AKSPKILPDI LKKIGDTPM VRINKIGKKF GLKCELLAKC EFFNAGGSVK DRISLRMIED AERDGTLKPG DTIIEPTSGN TGIGLALAAA V RGYRCIIV ...String: MPSETPQAEV GPTGCPHRSG PHSAKGSLEK GSPEDKEAKE PLWIRPDAPS RCTWQLGRPA SESPHHHTAP AKSPKILPDI LKKIGDTPM VRINKIGKKF GLKCELLAKC EFFNAGGSVK DRISLRMIED AERDGTLKPG DTIIEPTSGN TGIGLALAAA V RGYRCIIV MPEKMSSEKV DVLRALGAEI VRTPTNARFD SPESHVGVAW RLKNEIPNSH ILDQYRNASN PLAHYDTTAD EI LQQCDGK LDMLVASVGT GGTITGIARK LKEKCPGCRI IGVDPEGSIL AEPEELNQTE QTTYEVEGIG YDFIPTVLDR TVV DKWFKS NDEEAFTFAR MLIAQEGLLC GGSAGSTVAV AVKAAQELQE GQRCVVILPD SVRNYMTKFL SDRWMLQKGF LKEE DLTEK KPWWWHLRVQ ELGLSAPLTV LPTITCGHTI EILREKGFDQ APVVDEAGVI LGMVTLGNML SSLLAGKVQP SDQVG KVIY KQFKQIRLTD TLGRLSHILE MDHFALVVHE QIQYHSTGKS SQRQMVFGVV TAIDLLNFVA AQERDQKAAH HHHHH UniProtKB: ![]() |
-Macromolecule #2: S-ADENOSYLMETHIONINE
Macromolecule | Name: S-ADENOSYLMETHIONINE / type: ligand / ID: 2 / Number of copies: 10 / Formula: SAM |
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Molecular weight | Theoretical: 398.437 Da |
Chemical component information | ![]() ChemComp-SAM: |
-Experimental details
-Structure determination
Method | ![]() |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 0.75 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, 5 mM SAM | ||||||||||||||||||
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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: GIF Bioquantum |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11220 / Average exposure time: 3.53 sec. / Average electron dose: 39.96 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 79.15 | ||||||||
Output model | ![]() PDB-8s5m: |