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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9SPW

This is version 1.0 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

DOI: https://doi.org/10.1038/s41467-026-73198-7

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

Find similar proteins by:

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
GTEx: ENSG00000160200
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35520
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
GTEx: ENSG00000160200
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35520
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain I [auth C] Focus chain K [auth D]
SFG (Subject of Investigation/LOI) Query on SFG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F]	G [auth A] H [auth B] J [auth C] L [auth D] M [auth E] 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		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on 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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-29

Deposition Author(s):

Inayathulla, M.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	CRSII5_177195

Revision History (Full details and data files)

Version 1.0: 2026-07-29
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.