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- PDB-8s5j: Full-length human cystathionine beta-synthase, basal state, helic... -

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Basic information

Entry
Database: PDB / ID: 8s5j
TitleFull-length human cystathionine beta-synthase, basal state, helical reconstruction
ComponentsCystathionine beta-synthase
KeywordsTRANSFERASE / Filament / Allostery
Function / homology
Function and homology information


Cysteine formation from homocysteine / homocysteine catabolic process / cystathionine beta-synthase / modified amino acid binding / cystathionine beta-synthase activity / L-serine catabolic process / regulation of nitric oxide mediated signal transduction / Metabolism of ingested SeMet, Sec, MeSec into H2Se / cysteine biosynthetic process via cystathionine / carbon monoxide binding ...Cysteine formation from homocysteine / homocysteine catabolic process / cystathionine beta-synthase / modified amino acid binding / cystathionine beta-synthase activity / L-serine catabolic process / regulation of nitric oxide mediated signal transduction / Metabolism of ingested SeMet, Sec, MeSec into H2Se / cysteine biosynthetic process via cystathionine / carbon monoxide binding / hydrogen sulfide biosynthetic process / L-serine metabolic process / homocysteine metabolic process / cartilage development involved in endochondral bone morphogenesis / L-cysteine catabolic process / cerebellum morphogenesis / cysteine biosynthetic process / response to folic acid / endochondral ossification / transsulfuration / cysteine biosynthetic process from serine / nitric oxide binding / DNA protection / S-adenosyl-L-methionine binding / nitrite reductase (NO-forming) activity / regulation of JNK cascade / 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 / heme binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cystathionine beta-synthase, C-terminal domain / Cystathionine beta-synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily ...Cystathionine beta-synthase, C-terminal domain / Cystathionine beta-synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cystathionine beta-synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMcCorvie, T.J. / Yue, W.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: 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
DepositionFeb 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
C: Cystathionine beta-synthase
D: Cystathionine beta-synthase
E: Cystathionine beta-synthase
F: Cystathionine beta-synthase
G: Cystathionine beta-synthase
H: Cystathionine beta-synthase
I: Cystathionine beta-synthase
J: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)615,97120
Polymers609,80610
Non-polymers6,16510
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Cystathionine beta-synthase / Beta-thionase / Serine sulfhydrase


Mass: 60980.578 Da / Num. of mol.: 10
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: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Helical assembly of full-length human cystathionine beta-synthase in the basal state
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 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
IDConc.NameFormulaBuffer-ID
125 mMHEPES1
2200 mMsodium chlorideNaCl1
32 mMTCEP1
40.005 % (v/v)Tween-201
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1400 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.2particle selection
4cryoSPARC3.3.2CTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARC3.3.2initial Euler assignment
10cryoSPARC3.3.2final Euler assignment
11cryoSPARC3.3.2classification
12cryoSPARC3.3.23D reconstruction
13PHENIXmodel refinement
14ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -108 ° / Axial rise/subunit: 51 Å / Axial symmetry: D1
Particle selectionNum. of particles selected: 749213
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89761 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingB value: 28.16 / Protocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 4COO

4coo


Accession code: 4COO / Source name: PDB / Type: experimental model

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