8DO0

Cryo-EM structure of the human Sec61 complex inhibited by mycolactone


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A common mechanism of Sec61 translocon inhibition by small molecules.

Itskanov, S.Wang, L.Junne, T.Sherriff, R.Xiao, L.Blanchard, N.Shi, W.Q.Forsyth, C.Hoepfner, D.Spiess, M.Park, E.

(2023) Nat Chem Biol 19: 1063-1071

  • DOI: https://doi.org/10.1038/s41589-023-01337-y
  • Primary Citation of Related Structures:  
    8DNV, 8DNW, 8DNX, 8DNY, 8DNZ, 8DO0, 8DO1, 8DO2, 8DO3

  • PubMed Abstract: 

    The Sec61 complex forms a protein-conducting channel in the endoplasmic reticulum membrane that is required for secretion of soluble proteins and production of many membrane proteins. Several natural and synthetic small molecules specifically inhibit Sec61, generating cellular effects that are useful for therapeutic purposes, but their inhibitory mechanisms remain unclear. Here we present near-atomic-resolution structures of human Sec61 inhibited by a comprehensive panel of structurally distinct small molecules-cotransin, decatransin, apratoxin, ipomoeassin, mycolactone, cyclotriazadisulfonamide and eeyarestatin. All inhibitors bind to a common lipid-exposed pocket formed by the partially open lateral gate and plug domain of Sec61. Mutations conferring resistance to the inhibitors are clustered at this binding pocket. The structures indicate that Sec61 inhibitors stabilize the plug domain in a closed state, thereby preventing the protein-translocation pore from opening. Our study provides the atomic details of Sec61-inhibitor interactions and the structural framework for further pharmacological studies and drug design.


  • Organizational Affiliation

    Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA, UMR 7042, Mulhouse, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit gammaA [auth B]68Homo sapiensMutation(s): 0 
Gene Names: SEC61G
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P60059 (Homo sapiens)
Explore P60059 
Go to UniProtKB:  P60059
PHAROS:  P60059
GTEx:  ENSG00000132432 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60059
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit betaB [auth C]96Homo sapiensMutation(s): 0 
Gene Names: SEC61B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P60468 (Homo sapiens)
Explore P60468 
Go to UniProtKB:  P60468
PHAROS:  P60468
GTEx:  ENSG00000106803 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60468
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit alpha isoform 1C [auth A]476Homo sapiensMutation(s): 15 
Gene Names: SEC61A1SEC61A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P61619 (Homo sapiens)
Explore P61619 
Go to UniProtKB:  P61619
PHAROS:  P61619
GTEx:  ENSG00000058262 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61619
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q6B (Subject of Investigation/LOI)
Query on Q6B

Download Ideal Coordinates CCD File 
D [auth A][(6~{S},7~{S},9~{Z},12~{R})-12-[(~{Z},2~{S},6~{R},7~{R},9~{R})-4,6-dimethyl-7,9-bis(oxidanyl)dec-4-en-2-yl]-7,9-dimethyl-2-oxidanylidene-1-oxacyclododec-9-en-6-yl] (2~{E},4~{E},6~{E},8~{E},10~{E},12~{S},13~{S},15~{S})-4,6,10-trimethyl-12,13,15-tris(oxidanyl)hexadeca-2,4,6,8,10-pentaenoate
C44 H70 O9
WKTLNJXZVDLRTJ-RTCFGNHXSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONcryoSPARC3.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Vallee Foundation Inc.United States--
The Pew Charitable TrustsUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references