Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 12-mer - A2B2C2D2E2F2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A7B5 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 1252.67 kDa 
• Atom Count: 61818 
• Residue Count: 7678 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

6F0L

S. cerevisiae MCM double hexamer bound to duplex DNA

• DOI: 10.2210/pdb6F0L/pdb
• EMDataResource: EMD-3960

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C, synthetic construct
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2017-11-20 Released: 2017-12-06 
• Deposition Author(s): Abid Ali, F., Pye, V.E., Douglas, M.E., Locke, J., Nans, A., Diffley, J.F.X., Costa, A.

---

Experimental Data Snapshot

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

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

• PubMed: 29269875 
• 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. 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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM2	2, A	868	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: MCM2, YBL023C, YBL0438 EC: 3.6.4.12
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P29469  Go to UniProtKB:  P29469

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM3	3, B	971	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: MCM3, YEL032W, SYGP-ORF23 EC: 3.6.4.12
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P24279  Go to UniProtKB:  P24279

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM4	4, C	933	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: MCM4, CDC54, HCD21, YPR019W, YP9531.13 EC: 3.6.4.12
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30665  Go to UniProtKB:  P30665

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Minichromosome maintenance protein 5	5, D	775	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: MCM5, CDC46, YLR274W, L9328.1 EC: 3.6.4.12
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P29496  Go to UniProtKB:  P29496

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM6	6, E	1017	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: MCM6, YGL201C EC: 3.6.4.12
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53091  Go to UniProtKB:  P53091

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM7	7, F	845	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: MCM7, CDC47, YBR202W, YBR1441 EC: 3.6.4.12
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38132  Go to UniProtKB:  P38132

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (62-MER)	X	62	synthetic construct

Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (62-MER)	Y	62	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	3, 5, B, D	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-11-20 
• Released Date: 2017-12-06 
Deposition Author(s): Abid Ali, F., Pye, V.E., Douglas, M.E., Locke, J., Nans, A., Diffley, J.F.X., Costa, A.

Revision History 

• 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