7QCD

CryoEM structure of the Smc5/6-holocomplex (composite structure)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structure of the Smc5/6 holo-complex.

Hallett, S.T.Campbell Harry, I.Schellenberger, P.Zhou, L.Cronin, N.B.Baxter, J.Etheridge, T.J.Murray, J.M.Oliver, A.W.

(2022) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkac692
  • Primary Citation of Related Structures:  
    7QCD

  • PubMed Abstract: 
  • The Smc5/6 complex plays an essential role in the resolution of recombination intermediates formed during mitosis or meiosis, or as a result of the cellular response to replication stress. It also functions as a restriction factor preventing viral replication ...

    The Smc5/6 complex plays an essential role in the resolution of recombination intermediates formed during mitosis or meiosis, or as a result of the cellular response to replication stress. It also functions as a restriction factor preventing viral replication. Here, we report the cryogenic EM (cryo-EM) structure of the six-subunit budding yeast Smc5/6 holo-complex, reconstituted from recombinant proteins expressed in insect cells - providing both an architectural overview of the entire complex and an understanding of how the Nse1/3/4 subcomplex binds to the hetero-dimeric SMC protein core. In addition, we demonstrate that a region within the head domain of Smc5, equivalent to the 'W-loop' of Smc4 or 'F-loop' of Smc1, mediates an important interaction with Nse1. Notably, mutations that alter the surface-charge profile of the region of Nse1 which accepts the Smc5-loop, lead to a slow-growth phenotype and a global reduction in the chromatin-associated fraction of the Smc5/6 complex, as judged by single molecule localisation microscopy experiments in live yeast. Moreover, when taken together, our data indicates functional equivalence between the structurally unrelated KITE and HAWK accessory subunits associated with SMC complexes.


    Organizational Affiliation

    Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 5A1,093Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: SMC5YOL034W
UniProt
Find proteins for Q08204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ08204
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 6B1,114Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: SMC6RHC18YLR383WL3502.2
UniProt
Find proteins for Q12749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ12749
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
E3 SUMO-protein ligase MMS21C281Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MMS21NSE2YEL019C
EC: 2.3.2
UniProt
Find proteins for P38632 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38632
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural maintenance of chromosomes element 1D358Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSE1YLR007W
EC: 2.3.2.27
UniProt
Find proteins for Q07913 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ07913
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural maintenance of chromosome element 3E303Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSE3YDR288W
UniProt
Find proteins for Q05541 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ05541
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural maintenance of chromosome element 4F715Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSE4QRI2YDL105WD2354
UniProt
Find proteins for P43124 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP43124
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth C],
H [auth D],
I [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/PO18955/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release