9D6L | pdb_00009d6l

Human Sec61 complex inhibited by KZR-261

• PDB DOI: https://doi.org/10.2210/pdb9D6L/pdb
• EM Map EMD-46597: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-08-15 Released: 2025-07-23 
• Deposition Author(s): Park, E., Wang, L.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Pre-clinical characterization of novel multi-client inhibitors of Sec61 with broad anti-tumor activity

Lowe, E., Anderl, J.L., Bade, D., Delgado-Martin, C., Dong, C., Fan, R.A., Fang, Y., Jiang, J., Johnson, H.W., Kempema, A., McGilvray, P., McMinn, D., Millare, B., Muchamuel, T., Poweleit, N., Qian, Y., Rehan, S., Scapin, G., Sugahara, A., Tranter, D., Tuch, B., Wang, J., Wang, L., Whang, J.A., Zuno-Mitchell, P., Paavilainen, V.O., Park, E., Taunton, J., Kirk, C.J., Anand, N.K.

(2025) J Pharmacol Exp Ther : 103634

• DOI: https://doi.org/10.1016/j.jpet.2025.103634

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 70.71 kDa 
• Atom Count: 4,224 
• Modeled Residue Count: 540 
• Deposited Residue Count: 640 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein Sec61 subunit gamma	A [auth B]	68	Homo sapiens	Mutation(s): 0  Gene Names: SEC61G
UniProt & NIH Common Fund Data Resources
Find proteins for P60059 (Homo sapiens) Explore P60059  Go to UniProtKB:  P60059
PHAROS:  P60059 GTEx:  ENSG00000132432

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein Sec61 subunit beta	B [auth C]	96	Homo sapiens	Mutation(s): 0  Gene Names: SEC61B
UniProt & NIH Common Fund Data Resources
Find proteins for P60468 (Homo sapiens) Explore P60468  Go to UniProtKB:  P60468
PHAROS:  P60468 GTEx:  ENSG00000106803

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein Sec61 subunit alpha isoform 1	C [auth A]	476	Homo sapiens	Mutation(s): 15  Gene Names: SEC61A1, SEC61A
UniProt & NIH Common Fund Data Resources
Find proteins for P61619 (Homo sapiens) Explore P61619  Go to UniProtKB:  P61619
PHAROS:  P61619 GTEx:  ENSG00000058262

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1A2B (Subject of Investigation/LOI)	D [auth A]	4-{(3S)-9-(cyclohexylmethyl)-5-[(3R,5R)-4-(3-fluoro-5-methoxyphenyl)-3,5-dimethylpiperazine-1-sulfonyl]-3-methyl-1,5,9-triazacyclododecane-1-sulfonyl}-N,N-dimethylaniline C38 H61 F N6 O5 S2 LIDUHPAGWLBVCL-DCMFLLSESA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.5

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Park, E., Wang, L.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release