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 9SML | pdb_00009sml

Structure of trans-basal conformer of human CBS trapped in PLP-serine external aldemine intermediate (CBS-PLP-Ser)- by Helical approach


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 9SML

This is version 1.2 of the entry. See complete history. 

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

  • 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.


  • Organizational Affiliation: 
    • Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland. inayathulla.mohammed@epfl.ch.

Macromolecule Content 

  • Total Structure Weight: 344.12 kDa 
  • Atom Count: 23,970 
  • Modeled Residue Count: 3,042 
  • Deposited Residue Count: 3,060 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cystathionine beta-synthase
A, B, C, D, E
A, B, C, D, E, F
510Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35520
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
KOU
(Subject of Investigation/LOI)

Query on KOU



Download:Ideal Coordinates CCD File
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine
C11 H15 N2 O8 P
ZTQZHYMXYBDMIL-BIMOUXMDSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIXdev_5430

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland10.001.133

Revision History  (Full details and data files)

  • 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