[English] 日本語
Yorodumi- EMDB-19740: Full-length human cystathionine beta-synthase with C-terminal 6xH... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19740 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Full-length human cystathionine beta-synthase with C-terminal 6xHis-tag, SAM bound, activated state, helical reconstruction | |||||||||
Map data | Locally sharpened map | |||||||||
Sample |
| |||||||||
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 | helical reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | McCorvie TJ / Yue WW | |||||||||
Funding support | United Kingdom, 1 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_19740.map.gz | 8.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-19740-v30.xml emd-19740.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19740_fsc.xml | 13.5 KB | Display | FSC data file |
Images | emd_19740.png | 63 KB | ||
Masks | emd_19740_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-19740.cif.gz | 6.6 KB | ||
Others | emd_19740_additional_1.map.gz emd_19740_half_map_1.map.gz emd_19740_half_map_2.map.gz | 91.6 MB 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19740 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19740 | 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 (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_19740.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Locally sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_19740_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Sharpened map
File | emd_19740_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_19740_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_19740_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
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 |
---|---|
Components |
|
-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 |
---|---|
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: 10 / Enantiomer: LEVO / EC number: cystathionine beta-synthase |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 61.636426 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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: Cystathionine beta-synthase |
-Macromolecule #2: S-ADENOSYLMETHIONINE
Macromolecule | Name: S-ADENOSYLMETHIONINE / type: ligand / ID: 2 / Number of copies: 10 / Formula: SAM |
---|---|
Molecular weight | Theoretical: 398.437 Da |
Chemical component information | ChemComp-SAM: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.75 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm |
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 |
-Image processing
-Atomic model buiding 1
Initial model |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 79.15 | ||||||||
Output model | PDB-8s5m: |