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- EMDB-54925: Structure of trans-basal conformer of human CBS trapped in PLP-am... -

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Basic information

Entry
Database: EMDB / ID: EMD-54925
TitleStructure of trans-basal conformer of human CBS trapped in PLP-aminoacrylate intermediate state (CBS PLP-AA)- by Helical processing.
Map data
Sample
  • Complex: Oligomeric complex of human Cystathionine beta-synthase
    • Protein or peptide: Cystathionine beta-synthase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID
Keywordstranssulfuration pathway / L-serine hydro-lyase / heme-binding protein / CBS domain / LYASE
Function / homology
Function and homology information


Cysteine formation from homocysteine / L-homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / carbon monoxide binding / hydrogen sulfide biosynthetic process / L-serine catabolic process / homocysteine metabolic process ...Cysteine formation from homocysteine / L-homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / carbon monoxide binding / hydrogen sulfide biosynthetic process / L-serine catabolic process / homocysteine metabolic process / L-cysteine catabolic process / L-cysteine biosynthetic process / L-serine metabolic process / transsulfuration / nitric oxide binding / DNA protection / S-adenosyl-L-methionine binding / nitrite reductase (NO-forming) activity / oxygen binding / response to nutrient levels / cellular response to insulin stimulus / 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 / cytosol / cytoplasm
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
Cystathionine beta-synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsInayathulla M / Tomas M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for a filamentous morpheein model of human cystathionine beta-synthase.
Authors: Inayathulla Mohammed / Ela Mijatovic / Thilo Magnus Philipp / Lucia Janickova / Kelly Ascencao / Francisco J Asturias / Luis Alfonso Martinez-Cruz / Csaba Szabo / Henning Stahlberg / Tomas Majtan /
Abstract: Human cystathionine beta-synthase (CBS) is a vital enzyme that regulates sulfur amino acid metabolism, hydrogen sulfide production, and cellular redox balance. Using a multidisciplinary approach, we ...Human cystathionine beta-synthase (CBS) is a vital enzyme that regulates sulfur amino acid metabolism, hydrogen sulfide production, and cellular redox balance. Using a multidisciplinary approach, we demonstrate that CBS functions as a filamentous morpheein, with its stability, turnover, and activity governed by dynamic quaternary structural transitions. Three distinct filamentous assemblies were resolved by cryo-EM and are mediated by the oligomerization loop (residues 516-525): (i) ligand-free trans-dimers that form trans-basal filaments with basal stability and activity, (ii) adenosylornithine-bound cis-dimers that assemble into stabilized cis-basal filaments and (iii) S-adenosylmethionine-bound allo-dimers, which, together with cis-dimers, form highly stable, allo-activated stacked filaments. These reversible filamentous assemblies redefine CBS biology by integrating oligomerization and allosteric regulation within a morpheein framework. These findings provide a transformative perspective on CBS function and open avenues for pharmacological targeting of dysregulated CBS in various diseases including homocystinuria, cancer, and Down syndrome.
History
DepositionAug 28, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54925.png

Downloads & links

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Map

FileDownload / File: emd_54925.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 336 pix.
= 303.744 Å		0.9 Å/pix.
x 336 pix.
= 303.744 Å		0.9 Å/pix.
x 336 pix.
= 303.744 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.904 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0865
Minimum - Maximum-0.504322 - 0.9099751
Average (Standard dev.)0.0023400942 (±0.020941908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 303.744 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54925_msk_1.map
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Additional map: unsharpened map

Fileemd_54925_additional_1.map
Annotationunsharpened map
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Half map: #2

Fileemd_54925_half_map_1.map
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Half map: #1

Fileemd_54925_half_map_2.map
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Sample components

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Entire : Oligomeric complex of human Cystathionine beta-synthase

EntireName: Oligomeric complex of human Cystathionine beta-synthase
Components
  • Complex: Oligomeric complex of human Cystathionine beta-synthase
    • Protein or peptide: Cystathionine beta-synthase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID

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Supramolecule #1: Oligomeric complex of human Cystathionine beta-synthase

SupramoleculeName: Oligomeric complex of human Cystathionine beta-synthase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cystathionine beta-synthase

MacromoleculeName: Cystathionine beta-synthase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: cystathionine beta-synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.402684 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PLWIRPDAPS RCTWQLGRPA SESPHHHTAP AKSPKILPDI LKKIGDTPMV RINKIGKKFG LKCELLAKCE FFNAGGSVKD RISLRMIED AERDGTLKPG DTIIEPTSGN TGIGLALAAA VRGYRCIIVM PEKMSSEKVD VLRALGAEIV RTPTNARFDS P ESHVGVAW ...String:
PLWIRPDAPS RCTWQLGRPA SESPHHHTAP AKSPKILPDI LKKIGDTPMV RINKIGKKFG LKCELLAKCE FFNAGGSVKD RISLRMIED AERDGTLKPG DTIIEPTSGN TGIGLALAAA VRGYRCIIVM PEKMSSEKVD VLRALGAEIV RTPTNARFDS P ESHVGVAW RLKNEIPNSH ILDQYRNASN PLAHYDTTAD EILQQCDGKL DMLVASVGTG GTITGIARKL KEKCPGCRII GV DPEGSIL AEPEELNQTE QTTYEVEGIG YDFIPTVLDR TVVDKWFKSN DEEAFTFARM LIAQEGLLCG GSAGSTVAVA VKA AQELQE GQRCVVILPD SVRNYMTKFL SDRWMLQKGF LKEEDLTEKK PWWWHLRVQE LGLSAPLTVL PTITCGHTIE ILRE KGFDQ APVVDEAGVI LGMVTLGNML SSLLAGKVQP SDQVGKVIYK QFKQIRLTDT LGRLSHILEM DHFALVVHEQ IQYHS TGKS SQRQMVFGVV TAIDLLNFVA AQERDQ

UniProtKB: Cystathionine beta-synthase

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METH...

MacromoleculeName: 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID
type: ligand / ID: 3 / Number of copies: 6 / Formula: P1T
Molecular weightTheoretical: 318.22 Da
Chemical component information

ChemComp-P1T:
2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 50.48 Å
Applied symmetry - Helical parameters - Δ&Phi: -114.38 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 180000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab-initio
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9si8:
Structure of trans-basal conformer of human CBS trapped in PLP-aminoacrylate intermediate state (CBS PLP-AA)- by Helical processing.

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