6F0L

S. cerevisiae MCM double hexamer bound to duplex DNA

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Cryo-EM structure of a licensed DNA replication origin.

Abid Ali, F., Douglas, M.E., Locke, J., Pye, V.E., Nans, A., Diffley, J.F.X., Costa, A.

(2017) Nat Commun 8: 2241-2241

  • DOI: 10.1038/s41467-017-02389-0
  • Primary Citation of Related Structures:  
    6F0L

  • PubMed Abstract: 

    • Eukaryotic origins of replication are licensed upon loading of the MCM helicase motor onto DNA. ATP hydrolysis by MCM is required for loading and the post-catalytic MCM is an inactive double hexamer that encircles duplex DNA. Origin firing depends on MCM engagement of Cdc45 and GINS to form the CMG holo-helicase ...

    Eukaryotic origins of replication are licensed upon loading of the MCM helicase motor onto DNA. ATP hydrolysis by MCM is required for loading and the post-catalytic MCM is an inactive double hexamer that encircles duplex DNA. Origin firing depends on MCM engagement of Cdc45 and GINS to form the CMG holo-helicase. CMG assembly requires several steps including MCM phosphorylation by DDK. To understand origin activation, here we have determined the cryo-EM structures of DNA-bound MCM, either unmodified or phosphorylated, and visualize a phospho-dependent MCM element likely important for Cdc45 recruitment. MCM pore loops touch both the Watson and Crick strands, constraining duplex DNA in a bent configuration. By comparing our new MCM-DNA structure with the structure of CMG-DNA, we suggest how the conformational transition from the loaded, post-catalytic MCM to CMG might promote DNA untwisting and melting at the onset of replication.

    Organizational Affiliation: 

    Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. alessandro.costa@crick.ac.uk.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2],
G [auth A]		868Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM2, YBL023C, YBL0438
EC: 3.6.4.12
UniProt
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29469 
Go to UniProtKB:  P29469
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29469
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3],
H [auth B]		971Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM3, YEL032W, SYGP-ORF23
EC: 3.6.4.12
UniProt
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P24279 
Go to UniProtKB:  P24279
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24279
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4],
I [auth C]		933Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM4, CDC54, HCD21, YPR019W, YP9531.13
EC: 3.6.4.12
UniProt
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P30665 
Go to UniProtKB:  P30665
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30665
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5D [auth 5],
J [auth D]		775Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM5, CDC46, YLR274W, L9328.1
EC: 3.6.4.12
UniProt
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29496 
Go to UniProtKB:  P29496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29496
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6],
K [auth E]		1017Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM6, YGL201C
EC: 3.6.4.12
UniProt
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53091 
Go to UniProtKB:  P53091
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53091
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7],
L [auth F]		845Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM7, CDC47, YBR202W, YBR1441
EC: 3.6.4.12
UniProt
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38132 
Go to UniProtKB:  P38132
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38132
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (62-MER)M [auth X]62synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (62-MER)N [auth Y]62synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
O [auth 3],
P [auth 5],
Q [auth B],
R [auth D]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Database references
  • Version 1.2: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-11-20
    Changes: Database references
  • Version 1.4: 2019-12-11
    Changes: Other