9SQU | pdb_00009squ

Structure of trans-basal conformer of human CBS encompassing 16-18 dimer repeating units (in absence of substrate and allosteric ligand)- by Helical approach

PDB DOI: https://doi.org/10.2210/pdb9SQU/pdb
EM Map EMD-55117: 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: 4.80 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

Validation slider image for 9SQU

This is version 1.0 of the entry. See complete history.

Literature

Structure of trans-basal conformer of human CBS encompassing 16-18 dimer repeating units (in absence of substrate and allosteric ligand)- by Helical approach

Inayathulla, M., Tomas, M.

To be published.

Macromolecule Content

Total Structure Weight: 1,841.42 kDa
Atom Count: 119,640
Modeled Residue Count: 15,210
Deposited Residue Count: 16,500
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-synthase	A AA [auth a] B BA [auth b] C [auth E] A, AA [auth a], B, BA [auth b], C [auth E], CA [auth c], D [auth F], DA [auth d], E [auth C], F [auth D], G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	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 ZA [auth V] SDF format, chain YA [auth U] SDF format, chain XA [auth T] SDF format, chain WA [auth S] SDF format, chain VA [auth R] SDF format, chain UA [auth Q] SDF format, chain TA [auth P] SDF format, chain SA [auth O] SDF format, chain RA [auth N] SDF format, chain QA [auth M] SDF format, chain PA [auth L] SDF format, chain OA [auth K] SDF format, chain NA [auth J] SDF format, chain MA [auth I] SDF format, chain LA [auth H] SDF format, chain KA [auth G] SDF format, chain JA [auth D] SDF format, chain IA [auth C] SDF format, chain HB [auth d] SDF format, chain HA [auth F] SDF format, chain GB [auth c] SDF format, chain GA [auth E] SDF format, chain FB [auth b] SDF format, chain FA [auth B] SDF format, chain EB [auth a] SDF format, chain EA [auth A] SDF format, chain DB [auth Z] SDF format, chain CB [auth Y] SDF format, chain BB [auth X] SDF format, chain AB [auth W] MOL2 format, chain ZA [auth V] MOL2 format, chain YA [auth U] MOL2 format, chain XA [auth T] MOL2 format, chain WA [auth S] MOL2 format, chain VA [auth R] MOL2 format, chain UA [auth Q] MOL2 format, chain TA [auth P] MOL2 format, chain SA [auth O] MOL2 format, chain RA [auth N] MOL2 format, chain QA [auth M] MOL2 format, chain PA [auth L] MOL2 format, chain OA [auth K] MOL2 format, chain NA [auth J] MOL2 format, chain MA [auth I] MOL2 format, chain LA [auth H] MOL2 format, chain KA [auth G] MOL2 format, chain JA [auth D] MOL2 format, chain IA [auth C] MOL2 format, chain HB [auth d] MOL2 format, chain HA [auth F] MOL2 format, chain GB [auth c] MOL2 format, chain GA [auth E] MOL2 format, chain FB [auth b] MOL2 format, chain FA [auth B] MOL2 format, chain EB [auth a] MOL2 format, chain EA [auth A] MOL2 format, chain DB [auth Z] MOL2 format, chain CB [auth Y] MOL2 format, chain BB [auth X] MOL2 format, chain AB [auth W] mmCIF format, chain ZA [auth V] mmCIF format, chain YA [auth U] mmCIF format, chain XA [auth T] mmCIF format, chain WA [auth S] mmCIF format, chain VA [auth R] mmCIF format, chain UA [auth Q] mmCIF format, chain TA [auth P] mmCIF format, chain SA [auth O] mmCIF format, chain RA [auth N] mmCIF format, chain QA [auth M] mmCIF format, chain PA [auth L] mmCIF format, chain OA [auth K] mmCIF format, chain NA [auth J] mmCIF format, chain MA [auth I] mmCIF format, chain LA [auth H] mmCIF format, chain KA [auth G] mmCIF format, chain JA [auth D] mmCIF format, chain IA [auth C] mmCIF format, chain HB [auth d] mmCIF format, chain HA [auth F] mmCIF format, chain GB [auth c] mmCIF format, chain GA [auth E] mmCIF format, chain FB [auth b] mmCIF format, chain FA [auth B] mmCIF format, chain EB [auth a] mmCIF format, chain EA [auth A] mmCIF format, chain DB [auth Z] mmCIF format, chain CB [auth Y] mmCIF format, chain BB [auth X] mmCIF format, chain AB [auth W]	AB [auth W] BB [auth X] CB [auth Y] DB [auth Z] EA [auth A] AB [auth W], BB [auth X], CB [auth Y], DB [auth Z], EA [auth A], EB [auth a], FA [auth B], FB [auth b], GA [auth E], GB [auth c], HA [auth F], HB [auth d], IA [auth C], JA [auth D], KA [auth G], LA [auth H], MA [auth I], NA [auth J], OA [auth K], PA [auth L], QA [auth M], RA [auth N], SA [auth O], TA [auth P], UA [auth Q], VA [auth R], WA [auth S], XA [auth T], YA [auth U], ZA [auth V]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AB [auth W] Focus chain BB [auth X] Focus chain CB [auth Y] Focus chain DB [auth Z] Focus chain EA [auth A] Focus chain EB [auth a] Focus chain FA [auth B] Focus chain FB [auth b] Focus chain GA [auth E] Focus chain GB [auth c] Focus chain HA [auth F] Focus chain HB [auth d] Focus chain IA [auth C] Focus chain JA [auth D] Focus chain KA [auth G] Focus chain LA [auth H] Focus chain MA [auth I] Focus chain NA [auth J] Focus chain OA [auth K] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain RA [auth N] Focus chain SA [auth O] Focus chain TA [auth P] Focus chain UA [auth Q] Focus chain VA [auth R] Focus chain WA [auth S] Focus chain XA [auth T] Focus chain YA [auth U] Focus chain ZA [auth V] Interactions & Density Focus chain AB [auth W] Focus chain BB [auth X] Focus chain CB [auth Y] Focus chain DB [auth Z] Focus chain EA [auth A] Focus chain EB [auth a] Focus chain FA [auth B] Focus chain FB [auth b] Focus chain GA [auth E] Focus chain GB [auth c] Focus chain HA [auth F] Focus chain HB [auth d] Focus chain IA [auth C] Focus chain JA [auth D] Focus chain KA [auth G] Focus chain LA [auth H] Focus chain MA [auth I] Focus chain NA [auth J] Focus chain OA [auth K] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain RA [auth N] Focus chain SA [auth O] Focus chain TA [auth P] Focus chain UA [auth Q] Focus chain VA [auth R] Focus chain WA [auth S] Focus chain XA [auth T] Focus chain YA [auth U] Focus chain ZA [auth V]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
LLP Query on LLP	A, AA [auth a], B, BA [auth b], C [auth E] A, AA [auth a], B, BA [auth b], C [auth E], CA [auth c], D [auth F], DA [auth d], E [auth C], F [auth D], G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	LYS	Pyridoxal phosphate	C₁₄ H₂₂ N₃ O₇ P

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.80 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

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: 2026-11-04

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