5UDB

Structural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1.

Yuan, Z.Riera, A.Bai, L.Sun, J.Nandi, S.Spanos, C.Chen, Z.A.Barbon, M.Rappsilber, J.Stillman, B.Speck, C.Li, H.

(2017) Nat. Struct. Mol. Biol. 24: 316-324

  • DOI: 10.1038/nsmb.3372
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To initiate DNA replication, the origin recognition complex (ORC) and Cdc6 load an Mcm2-7 double hexamer onto DNA. Without ATP hydrolysis, ORC-Cdc6 recruits one Cdt1-bound Mcm2-7 hexamer, thus forming an ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) helicase-loading i ...

    To initiate DNA replication, the origin recognition complex (ORC) and Cdc6 load an Mcm2-7 double hexamer onto DNA. Without ATP hydrolysis, ORC-Cdc6 recruits one Cdt1-bound Mcm2-7 hexamer, thus forming an ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) helicase-loading intermediate. Here we report a 3.9-Å structure of Saccharomyces cerevisiae OCCM on DNA. Flexible Mcm2-7 winged-helix domains (WHDs) engage ORC-Cdc6. A three-domain Cdt1 configuration embraces Mcm2, Mcm4, and Mcm6, thus comprising nearly half of the hexamer. The Cdt1 C-terminal domain extends to the Mcm6 WHD, which binds the Orc4 WHD. DNA passes through the ORC-Cdc6 and Mcm2-7 rings. Origin DNA interaction is mediated by an α-helix within Orc4 and positively charged loops within Orc2 and Cdc6. The Mcm2-7 C-tier AAA+ ring is topologically closed by an Mcm5 loop that embraces Mcm2, but the N-tier-ring Mcm2-Mcm5 interface remains open. This structure suggests a loading mechanism of the first Cdt1-bound Mcm2-7 hexamer by ORC-Cdc6.


    Organizational Affiliation

    Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM2
2
868Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM2
EC: 3.6.4.12
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM2
Go to UniProtKB:  P29469
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM3
3
971Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM3
EC: 3.6.4.12
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM3
Go to UniProtKB:  P24279
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM4
4
933Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM4 (CDC54, HCD21)
EC: 3.6.4.12
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM4
Go to UniProtKB:  P30665
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Minichromosome maintenance protein 5
5
775Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM5 (CDC46)
EC: 3.6.4.12
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM5
Go to UniProtKB:  P29496
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM6
6
1017Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM6
EC: 3.6.4.12
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM6
Go to UniProtKB:  P53091
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM7
7
845Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM7 (CDC47)
EC: 3.6.4.12
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM7
Go to UniProtKB:  P38132
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cell division cycle protein CDT1
8
604Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TAH11 (CDT1, SID2)
Find proteins for P47112 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47112
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cell division control protein 6
9
513Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CDC6
Find proteins for P09119 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CDC6
Go to UniProtKB:  P09119
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 1
A
914Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC1
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC1
Go to UniProtKB:  P54784
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 2
B
620Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC2 (RRR1, SIR5)
Find proteins for P32833 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC2
Go to UniProtKB:  P32833
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 3
C
616Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC3 (OAF1, OIF1)
Find proteins for P54790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC3
Go to UniProtKB:  P54790
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 4
D
529Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC4
Find proteins for P54791 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC4
Go to UniProtKB:  P54791
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 5
E
479Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC5
Find proteins for P50874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC5
Go to UniProtKB:  P50874
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 6
F
435Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC6 (AAP1)
Find proteins for P38826 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC6
Go to UniProtKB:  P38826
Entity ID: 15
MoleculeChainsLengthOrganism
DNA (39-MER)M39synthetic construct
Entity ID: 16
MoleculeChainsLengthOrganism
DNA (39-MER)N39synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download SDF File 
Download CCD File 
2, 3, 6, 7, 9, A, D, E
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM111472
National Institutes of Health/Office of the DirectorUnited StatesOD12272
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM45436
Biotechnology and Biological Sciences Research CouncilUnited KingdomP56061
Wellcome TrustUnited KingdomP56628

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-15
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Data collection
  • Version 1.3: 2017-11-08
    Type: Derived calculations