9SPW | pdb_00009spw

Structure of cis-basal conformer of human CBS induced by non-activating allosteric SAO ligand - by single particle approach.

• PDB DOI: https://doi.org/10.2210/pdb9SPW/pdb
• EM Map EMD-55099: EMDB EMDataResource

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-18 Released: 2026-07-29 
• Deposition Author(s): Inayathulla, M., Tomas, M.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.11 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for a filamentous morpheein model of human cystathionine beta-synthase.

Mohammed, I., Mijatovic, E., Philipp, T.M., Janickova, L., Ascencao, K., Asturias, F.J., Martinez-Cruz, L.A., Szabo, C., Stahlberg, H., Majtan, T.

(2026) Nat Commun 17

• PubMed: 42248820 
• DOI: https://doi.org/10.1038/s41467-026-73198-7
• Primary Citation Related Structures: 
  9SHM, 9SHN, 9SI8, 9SML, 9SPV, 9SPW, 9SQ0, 9SQQ


• PubMed 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 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.

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Organizational Affiliation: 
• Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland. [e-mail].
Laboratory of Biological Electron Microscopy, Department of Fundamental Microbiology, Faculty of Medicine and Biology, University of Lausanne, Lausanne, Switzerland. [e-mail].
Dubochet Center for Imaging Lausanne, University of Lausanne, Lausanne, Switzerland. [e-mail].
Section of Pharmacology, Department of Oncology, Microbiology and Immunology, University of Fribourg, Fribourg, Switzerland.
Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
Laboratory of Biological Electron Microscopy, Department of Fundamental Microbiology, Faculty of Medicine and Biology, University of Lausanne, Lausanne, Switzerland.
Section of Pharmacology, Department of Oncology, Microbiology and Immunology, University of Fribourg, Fribourg, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 368.65 kDa 
• Atom Count: 12,194 
• Modeled Residue Count: 1,554 
• Deposited Residue Count: 3,306 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-synthase	A	551	Homo sapiens	Mutation(s): 0  Gene Names: CBS EC: 4.2.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for P35520 (Homo sapiens) Explore P35520  Go to UniProtKB:  P35520
PHAROS:  P35520 GTEx:  ENSG00000160200

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-synthase	B, C, D, E, F	551	Homo sapiens	Mutation(s): 0  Gene Names: CBS EC: 4.2.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for P35520 (Homo sapiens) Explore P35520  Go to UniProtKB:  P35520
PHAROS:  P35520 GTEx:  ENSG00000160200

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SFG (Subject of Investigation/LOI)	G [auth A], H [auth B], J [auth C], L [auth D], M [auth E], N [auth F]	SINEFUNGIN C15 H23 N7 O5 LMXOHSDXUQEUSF-YECHIGJVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	B, C, D, E, F	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.11 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_5430
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-29 
Deposition Author(s): Inayathulla, M., Tomas, M.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	CRSII5_177195

Revision History  

• Version 1.0: 2026-07-29
  Type: Initial release
  
• Version 1.1: 2026-08-05
  Changes: Data collection, Database references
• Version 1.2: 2026-09-02
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Data collection, Derived calculations, Structure summary