8B9B

S. cerevisiae replisome + Ctf4, bound by pol alpha. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

How Pol alpha-primase is targeted to replisomes to prime eukaryotic DNA replication.

Jones, M.L.Aria, V.Baris, Y.Yeeles, J.T.P.

(2023) Mol Cell 83: 2911

  • DOI: https://doi.org/10.1016/j.molcel.2023.06.035
  • Primary Citation of Related Structures:  
    8B9A, 8B9B, 8B9C, 8B9D

  • PubMed Abstract: 

    During eukaryotic DNA replication, Pol α-primase generates primers at replication origins to start leading-strand synthesis and every few hundred nucleotides during discontinuous lagging-strand replication. How Pol α-primase is targeted to replication forks to prime DNA synthesis is not fully understood. Here, by determining cryoelectron microscopy (cryo-EM) structures of budding yeast and human replisomes containing Pol α-primase, we reveal a conserved mechanism for the coordination of priming by the replisome. Pol α-primase binds directly to the leading edge of the CMG (CDC45-MCM-GINS) replicative helicase via a complex interaction network. The non-catalytic PRIM2/Pri2 subunit forms two interfaces with CMG that are critical for in vitro DNA replication and yeast cell growth. These interactions position the primase catalytic subunit PRIM1/Pri1 directly above the exit channel for lagging-strand template single-stranded DNA (ssDNA), revealing why priming occurs efficiently only on the lagging-strand template and elucidating a mechanism for Pol α-primase to overcome competition from RPA to initiate primer synthesis.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2]868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM2YBL023CYBL0438
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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]1,009Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4]933Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5D [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM5CDC46YLR274WL9328.1
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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6]1,017Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM6YGL201C
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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase large subunitG [auth A]528Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRI2YKL045WYKL258
UniProt
Find proteins for P20457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20457 
Go to UniProtKB:  P20457
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20457
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha subunit BH [auth B]705Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL12YBL035CYBL0414
UniProt
Find proteins for P38121 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38121 
Go to UniProtKB:  P38121
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38121
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1I [auth C]208Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF1YDR013WPZA208YD8119.18
UniProt
Find proteins for Q12488 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12488 
Go to UniProtKB:  Q12488
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12488
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2J [auth D]213Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF2YJL072CHRF213J1086
UniProt
Find proteins for P40359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40359 
Go to UniProtKB:  P40359
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40359
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3K [auth E]217Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF3YOL146W
UniProt
Find proteins for Q12146 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12146 
Go to UniProtKB:  Q12146
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12146
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5L [auth F]294Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLD5YDR489W
UniProt
Find proteins for Q03406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03406 
Go to UniProtKB:  Q03406
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03406
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 45M [auth G]657Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC45SLD4YLR103CL8004.11
UniProt
Find proteins for Q08032 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08032 
Go to UniProtKB:  Q08032
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08032
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunit AN [auth J]1,468Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL1CDC17YNL102WN2181
EC: 2.7.7.7
UniProt
Find proteins for P13382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13382 
Go to UniProtKB:  P13382
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13382
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of replication checkpoint protein 1O [auth P]1,109Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MRC1YCL061CYCL61C/YCL60C
UniProt
Find proteins for P25588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25588 
Go to UniProtKB:  P25588
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25588
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase small subunitR [auth S]444Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRI1YIR008CYIB8C
EC: 2.7.7
UniProt
Find proteins for P10363 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10363 
Go to UniProtKB:  P10363
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10363
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Topoisomerase 1-associated factor 1S [auth X]1,238Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOF1YNL273WN0636
UniProt
Find proteins for P53840 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53840 
Go to UniProtKB:  P53840
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53840
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome segregation in meiosis protein 3T [auth Y]319Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CSM3YMR048WYM9796.01
UniProt
Find proteins for Q04659 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04659 
Go to UniProtKB:  Q04659
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04659
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha-binding proteinU [auth H],
V [auth L],
W [auth K]
962Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF4CHL15POB1YPR135WP9659.7
UniProt
Find proteins for Q01454 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01454 
Go to UniProtKB:  Q01454
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01454
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains LengthOrganismImage
Leading strand DNAP [auth Q]84Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains LengthOrganismImage
Lagging strand DNAQ [auth R]106Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
AA [auth 4],
GA [auth 7],
X [auth 2],
Z [auth 3]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth 4],
EA [auth 5],
FA [auth 6],
IA [auth 7]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth 4],
DA [auth 5],
HA [auth 7],
Y [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20_4459:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/12

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references