7NJ1 | pdb_00007nj1

CryoEM structure of the human Separase-Securin complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7NJ1

This is version 2.0 of the entry. See complete history

Literature

Structural basis of human separase regulation by securin and CDK1-cyclin B1.

Yu, J.Raia, P.Ghent, C.M.Raisch, T.Sadian, Y.Cavadini, S.Sabale, P.M.Barford, D.Raunser, S.Morgan, D.O.Boland, A.

(2021) Nature 596: 138-142

  • DOI: https://doi.org/10.1038/s41586-021-03764-0
  • Primary Citation Related Structures: 
    7NJ0, 7NJ1

  • PubMed Abstract: 

    In early mitosis, the duplicated chromosomes are held together by the ring-shaped cohesin complex 1 . Separation of chromosomes during anaphase is triggered by separase-a large cysteine endopeptidase that cleaves the cohesin subunit SCC1 (also known as RAD21 2-4 ). Separase is activated by degradation of its inhibitors, securin 5 and cyclin B 6 , but the molecular mechanisms of separase regulation are not clear. Here we used cryogenic electron microscopy to determine the structures of human separase in complex with either securin or CDK1-cyclin B1-CKS1. In both complexes, separase is inhibited by pseudosubstrate motifs that block substrate binding at the catalytic site and at nearby docking sites. As in Caenorhabditis elegans 7 and yeast 8 , human securin contains its own pseudosubstrate motifs. By contrast, CDK1-cyclin B1 inhibits separase by deploying pseudosubstrate motifs from intrinsically disordered loops in separase itself. One autoinhibitory loop is oriented by CDK1-cyclin B1 to block the catalytic sites of both separase and CDK1 9,10 . Another autoinhibitory loop blocks substrate docking in a cleft adjacent to the separase catalytic site. A third separase loop contains a phosphoserine 6 that promotes complex assembly by binding to a conserved phosphate-binding pocket in cyclin B1. Our study reveals the diverse array of mechanisms by which securin and CDK1-cyclin B1 bind and inhibit separase, providing the molecular basis for the robust control of chromosome segregation.


  • Organizational Affiliation
    • Department of Molecular Biology, University of Geneva, Geneva, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 259.66 kDa 
  • Atom Count: 11,273 
  • Modeled Residue Count: 1,501 
  • Deposited Residue Count: 2,362 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Separin2,160Homo sapiensMutation(s): 0 
Gene Names: ESPL1ESP1KIAA0165
EC: 3.4.22.49
UniProt & NIH Common Fund Data Resources
Find proteins for Q14674 (Homo sapiens)
Explore Q14674 
Go to UniProtKB:  Q14674
PHAROS:  Q14674
GTEx:  ENSG00000135476 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14674
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Securin202Homo sapiensMutation(s): 0 
Gene Names: PTTG1EAP1PTTGTUTR1
UniProt & NIH Common Fund Data Resources
Find proteins for O95997 (Homo sapiens)
Explore O95997 
Go to UniProtKB:  O95997
PHAROS:  O95997
GTEx:  ENSG00000164611 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95997
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_185235
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM118053

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 2.0: 2025-10-01
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary