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- EMDB-19739: Full-length human cystathionine beta-synthase, basal state, parti... -
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Open data
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Basic information
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Title | Full-length human cystathionine beta-synthase, basal state, partially degraded tetramer | |||||||||
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![]() | Filament / Allostery / TRANSFERASE | |||||||||
Function / homology | ![]() Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process / cystathionine beta-synthase activity ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process / cystathionine beta-synthase activity / L-serine metabolic process / cartilage development involved in endochondral bone morphogenesis / regulation of nitric oxide mediated signal transduction / cysteine biosynthetic process / L-cysteine catabolic process / cerebellum morphogenesis / cysteine synthase activity / L-cysteine desulfhydrase activity / nitric oxide binding / cysteine biosynthetic process from serine / DNA protection / L-serine catabolic process / endochondral ossification / transsulfuration / S-adenosyl-L-methionine binding / response to folic acid / nitrite reductase (NO-forming) activity / superoxide metabolic process / blood vessel remodeling / maternal process involved in female pregnancy / 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 / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | 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 | ![]() | 450.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.4 KB 22.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.7 KB | Display | ![]() |
Images | ![]() | 55.2 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() | 237.5 MB 442.2 MB 442.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 33.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8s5lMC ![]() 8s5hC ![]() 8s5iC ![]() 8s5jC ![]() 8s5kC ![]() 8s5mC 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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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
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-Additional map: non-sharpened map
File | emd_19739_additional_1.map | ||||||||||||
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Annotation | non-sharpened map | ||||||||||||
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-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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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-#2 |
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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: 2 / Enantiomer: LEVO / EC number: cystathionine beta-synthase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 60.980578 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: Cystathionine beta-synthase
Macromolecule | Name: Cystathionine beta-synthase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: cystathionine beta-synthase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 60.752453 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SMPSETPQAE VGPTGCPHRS GPHSAKGSLE KGSPEDKEAK EPLWIRPDAP SRCTWQLGRP ASESPHHHTA PAKSPKILPD ILKKIGDTP MVRINKIGKK FGLKCELLAK CEFFNAGGSV KDRISLRMIE DAERDGTLKP GDTIIEPTSG NTGIGLALAA A VRGYRCII ...String: SMPSETPQAE VGPTGCPHRS GPHSAKGSLE KGSPEDKEAK EPLWIRPDAP SRCTWQLGRP ASESPHHHTA PAKSPKILPD ILKKIGDTP MVRINKIGKK FGLKCELLAK CEFFNAGGSV KDRISLRMIE DAERDGTLKP GDTIIEPTSG NTGIGLALAA A VRGYRCII VMPEKMSSEK VDVLRALGAE IVRTPTNARF DSPESHVGVA WRLKNEIPNS HILDQYRNAS NPLAHYDTTA DE ILQQCDG KLDMLVASVG TGGTITGIAR KLKEKCPGCR IIGVDPEGSI LAEPEELNQT EQTTYEVEGI GYDFIPTVLD RTV VDKWFK SNDEEAFTFA RMLIAQEGLL CGGSAGSTVA VAVKAAQELQ EGQRCVVILP DSVRNYMTKF LSDRWMLQKG FLKE EDLTE KKPWWWHLRV QELGLSAPLT VLPTITCGHT IEILREKGFD QAPVVDEAGV ILGMVTLGNM LSSLLAGKVQ PSDQV GKVI YKQFKQIRLT DTLGRLSHIL EMDHFALVVH EQIQYHSTGK SSQRQMVFGV VTAIDLLNFV AAQERDQK UniProtKB: Cystathionine beta-synthase |
-Macromolecule #3: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 3 / Number of copies: 4 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ![]() ChemComp-HEM: |
-Macromolecule #4: PYRIDOXAL-5'-PHOSPHATE
Macromolecule | Name: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: PLP |
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Molecular weight | Theoretical: 247.142 Da |
Chemical component information | ![]() ChemComp-PLP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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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 |
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Electron microscopy
Microscope | TFS GLACIOS |
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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 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 |