6WGC

Atomic model of semi-attached mutant OCCM-DNA complex (ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD truncation)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 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 mechanism of helicase loading onto replication origin DNA by ORC-Cdc6.

Yuan, Z.Schneider, S.Dodd, T.Riera, A.Bai, L.Yan, C.Magdalou, I.Ivanov, I.Stillman, B.Li, H.Speck, C.

(2020) Proc Natl Acad Sci U S A 117: 17747-17756

  • DOI: 10.1073/pnas.2006231117
  • Primary Citation of Related Structures:  
    6WGC, 6WGF, 6WGG, 6WGI

  • PubMed Abstract: 
  • DNA replication origins serve as sites of replicative helicase loading. In all eukaryotes, the six-subunit origin recognition complex (Orc1-6; ORC) recognizes the replication origin. During late M-phase of the cell-cycle, Cdc6 binds to ORC and the ORC-Cdc6 complex loads in a multistep reaction and, with the help of Cdt1, the core Mcm2-7 helicase onto DNA ...

    DNA replication origins serve as sites of replicative helicase loading. In all eukaryotes, the six-subunit origin recognition complex (Orc1-6; ORC) recognizes the replication origin. During late M-phase of the cell-cycle, Cdc6 binds to ORC and the ORC-Cdc6 complex loads in a multistep reaction and, with the help of Cdt1, the core Mcm2-7 helicase onto DNA. A key intermediate is the ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) complex in which DNA has been already inserted into the central channel of Mcm2-7. Until now, it has been unclear how the origin DNA is guided by ORC-Cdc6 and inserted into the Mcm2-7 hexamer. Here, we truncated the C-terminal winged-helix-domain (WHD) of Mcm6 to slow down the loading reaction, thereby capturing two loading intermediates prior to DNA insertion in budding yeast. In "semi-attached OCCM," the Mcm3 and Mcm7 WHDs latch onto ORC-Cdc6 while the main body of the Mcm2-7 hexamer is not connected. In "pre-insertion OCCM," the main body of Mcm2-7 docks onto ORC-Cdc6, and the origin DNA is bent and positioned adjacent to the open DNA entry gate, poised for insertion, at the Mcm2-Mcm5 interface. We used molecular simulations to reveal the dynamic transition from preloading conformers to the loaded conformers in which the loading of Mcm2-7 on DNA is complete and the DNA entry gate is fully closed. Our work provides multiple molecular insights into a key event of eukaryotic DNA replication.


    Organizational Affiliation

    MRC London Institute of Medical Sciences (LMS), W12 0NN London, United Kingdom.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 6A [auth 9]513Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC6YJL194WJ0347
UniProt
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UniProt GroupP09119
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 1B [auth A]913Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC1YML065W
UniProt
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 2C [auth B]620Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC2RRR1SIR5YBR060CYBR0523
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 3D [auth C]616Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC3OAF1OIF1YLL004WL1365
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 5E479Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC5YNL261WN0834
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 4F [auth D]529Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC4YPR162CP9325.5
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 6G [auth F]435Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC6AAP1YHR118C
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3H [auth 3]971Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7I [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
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Entity ID: 10
MoleculeChainsLengthOrganismImage
DNA (41-MER)J [auth G]41Saccharomyces cerevisiae
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Entity ID: 11
MoleculeChainsLengthOrganismImage
DNA (41-MER)K [auth H]41Saccharomyces cerevisiae
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
L [auth 9],
M [auth A],
N [auth E],
O [auth D]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110387
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131754
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S001387/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/N000323/1
Wellcome TrustUnited Kingdom107903/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Structure summary
  • Version 1.2: 2020-07-29
    Changes: Database references
  • Version 1.3: 2020-08-12
    Changes: Database references