5V8F

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 1.2 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

    MRC London Institute of Medical Sciences (LMS), London, UK.,Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.,DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.




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
800Saccharomyces 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
913Saccharomyces 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 StatesGM111742
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: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2017-11-08
    Type: Derived calculations, Experimental preparation