9SR3 | pdb_00009sr3

Structure of stacked allo-activated CBS conformer by allosteric SAM - by Helical approach

PDB DOI: https://doi.org/10.2210/pdb9SR3/pdb
EM Map EMD-55128: EMDB EMDataResource

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

Deposited: 2025-09-23 Released: 2026-11-04
Deposition Author(s): Inayathulla, M., Tomas, M.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 8.50 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

Validation slider image for 9SR3

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 17: 7221

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

Macromolecule Content

Total Structure Weight: 3,047.68 kDa
Atom Count: 97,686
Modeled Residue Count: 12,645
Deposited Residue Count: 27,500
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-synthase	A [auth b] B [auth a] C [auth f] D [auth e] E [auth j] A [auth b], B [auth a], C [auth f], D [auth e], E [auth j], F [auth i], G [auth d], H [auth c], I [auth h], J [auth g], K [auth l], L [auth k], M [auth B], N [auth A], O [auth F], P [auth E], Q [auth J], R [auth I], S [auth D], T [auth C], U [auth H], V [auth G], W [auth L], X [auth K]	550	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 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	AA [auth O] BA [auth P] CA [auth Q] DA [auth R] EA [auth m] AA [auth O], BA [auth P], CA [auth Q], DA [auth R], EA [auth m], FA [auth S], GA [auth T], HA [auth U], IA [auth V], JA [auth W], KA [auth X], LA [auth Y], MA [auth Z], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], WA [auth w], XA [auth x], Y [auth M], Z [auth N]	550	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 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 1 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 AB [auth O] SDF format, chain BB [auth P] SDF format, chain CB [auth Q] SDF format, chain DB [auth R] SDF format, chain EB [auth m] SDF format, chain FB [auth S] SDF format, chain GB [auth T] SDF format, chain IB [auth V] SDF format, chain JB [auth W] SDF format, chain KB [auth X] SDF format, chain LB [auth Y] SDF format, chain MB [auth Z] SDF format, chain NB [auth n] SDF format, chain PB [auth p] SDF format, chain QB [auth q] SDF format, chain RB [auth r] SDF format, chain SB [auth s] SDF format, chain TB [auth t] SDF format, chain UB [auth u] SDF format, chain WB [auth w] SDF format, chain XB [auth x] SDF format, chain ZA [auth N] SDF format, chain YA [auth M] SDF format, chain VB [auth v] SDF format, chain OB [auth o] SDF format, chain HB [auth U] MOL2 format, chain AB [auth O] MOL2 format, chain BB [auth P] MOL2 format, chain CB [auth Q] MOL2 format, chain DB [auth R] MOL2 format, chain EB [auth m] MOL2 format, chain FB [auth S] MOL2 format, chain GB [auth T] MOL2 format, chain IB [auth V] MOL2 format, chain JB [auth W] MOL2 format, chain KB [auth X] MOL2 format, chain LB [auth Y] MOL2 format, chain MB [auth Z] MOL2 format, chain NB [auth n] MOL2 format, chain PB [auth p] MOL2 format, chain QB [auth q] MOL2 format, chain RB [auth r] MOL2 format, chain SB [auth s] MOL2 format, chain TB [auth t] MOL2 format, chain UB [auth u] MOL2 format, chain WB [auth w] MOL2 format, chain XB [auth x] MOL2 format, chain ZA [auth N] MOL2 format, chain YA [auth M] MOL2 format, chain VB [auth v] MOL2 format, chain OB [auth o] MOL2 format, chain HB [auth U] mmCIF format, chain AB [auth O] mmCIF format, chain BB [auth P] mmCIF format, chain CB [auth Q] mmCIF format, chain DB [auth R] mmCIF format, chain EB [auth m] mmCIF format, chain FB [auth S] mmCIF format, chain GB [auth T] mmCIF format, chain IB [auth V] mmCIF format, chain JB [auth W] mmCIF format, chain KB [auth X] mmCIF format, chain LB [auth Y] mmCIF format, chain MB [auth Z] mmCIF format, chain NB [auth n] mmCIF format, chain PB [auth p] mmCIF format, chain QB [auth q] mmCIF format, chain RB [auth r] mmCIF format, chain SB [auth s] mmCIF format, chain TB [auth t] mmCIF format, chain UB [auth u] mmCIF format, chain WB [auth w] mmCIF format, chain XB [auth x] mmCIF format, chain ZA [auth N] mmCIF format, chain YA [auth M] mmCIF format, chain VB [auth v] mmCIF format, chain OB [auth o] mmCIF format, chain HB [auth U]	AB [auth O] BB [auth P] CB [auth Q] DB [auth R] EB [auth m] AB [auth O], BB [auth P], CB [auth Q], DB [auth R], EB [auth m], FB [auth S], GB [auth T], HB [auth U], IB [auth V], JB [auth W], KB [auth X], LB [auth Y], MB [auth Z], NB [auth n], OB [auth o], PB [auth p], QB [auth q], RB [auth r], SB [auth s], TB [auth t], UB [auth u], VB [auth v], WB [auth w], XB [auth x], YA [auth M], ZA [auth N]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AB [auth O] Focus chain BB [auth P] Focus chain CB [auth Q] Focus chain DB [auth R] Focus chain EB [auth m] Focus chain FB [auth S] Focus chain GB [auth T] Focus chain HB [auth U] Focus chain IB [auth V] Focus chain JB [auth W] Focus chain KB [auth X] Focus chain LB [auth Y] Focus chain MB [auth Z] Focus chain NB [auth n] Focus chain OB [auth o] Focus chain PB [auth p] Focus chain QB [auth q] Focus chain RB [auth r] Focus chain SB [auth s] Focus chain TB [auth t] Focus chain UB [auth u] Focus chain VB [auth v] Focus chain WB [auth w] Focus chain XB [auth x] Focus chain YA [auth M] Focus chain ZA [auth N] Interactions & Density Focus chain AB [auth O] Focus chain BB [auth P] Focus chain CB [auth Q] Focus chain DB [auth R] Focus chain EB [auth m] Focus chain FB [auth S] Focus chain GB [auth T] Focus chain HB [auth U] Focus chain IB [auth V] Focus chain JB [auth W] Focus chain KB [auth X] Focus chain LB [auth Y] Focus chain MB [auth Z] Focus chain NB [auth n] Focus chain OB [auth o] Focus chain PB [auth p] Focus chain QB [auth q] Focus chain RB [auth r] Focus chain SB [auth s] Focus chain TB [auth t] Focus chain UB [auth u] Focus chain VB [auth v] Focus chain WB [auth w] Focus chain XB [auth x] Focus chain YA [auth M] Focus chain ZA [auth N]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
LLP Query on LLP	AA [auth O], BA [auth P], CA [auth Q], DA [auth R], EA [auth m] AA [auth O], BA [auth P], CA [auth Q], DA [auth R], EA [auth m], FA [auth S], GA [auth T], HA [auth U], IA [auth V], JA [auth W], KA [auth X], LA [auth Y], MA [auth Z], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], WA [auth w], XA [auth x], Y [auth M], Z [auth N]	LYS	Pyridoxal phosphate	C₁₄ H₂₂ N₃ O₇ P

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 8.50 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_5430
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Inayathulla, M.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	10.001.133

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release