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- PDB-8b9d: Human replisome bound by Pol Alpha -

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Entry
Database: PDB / ID: 8b9d
TitleHuman replisome bound by Pol Alpha
Components
  • (DNA polymerase alpha ...) x 2
  • (DNA replication complex GINS protein ...) x 4
  • (DNA replication licensing factor ...) x 6
  • Cell division control protein 45 homolog
  • Claspin
  • DNA Molecule
  • DNA primase large subunit
  • DNA primase small subunit
  • Leading strand DNA
  • Protein timeless homolog
  • TIMELESS-interacting protein
  • WD repeat and HMG-box DNA-binding protein 1
KeywordsREPLICATION / human / priming / polymerase
Function / homology
Function and homology information


cellular response to bleomycin / DNA primase AEP / DNA secondary structure binding / ribonucleotide binding / detection of abiotic stimulus / regulation of nuclear cell cycle DNA replication / replication fork arrest / Switching of origins to a post-replicative state / cell cycle phase transition / Unwinding of DNA ...cellular response to bleomycin / DNA primase AEP / DNA secondary structure binding / ribonucleotide binding / detection of abiotic stimulus / regulation of nuclear cell cycle DNA replication / replication fork arrest / Switching of origins to a post-replicative state / cell cycle phase transition / Unwinding of DNA / DNA replication initiation / DNA strand elongation involved in mitotic DNA replication / GINS complex / mitotic DNA replication preinitiation complex assembly / activation of protein kinase activity / Telomere C-strand synthesis initiation / DNA/RNA hybrid binding / cellular response to cisplatin / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / replication fork protection complex / nuclear origin of replication recognition complex / cellular response to hydroxyurea / regulation of type I interferon production / alpha DNA polymerase:primase complex / anaphase-promoting complex binding / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / mitotic DNA replication / DNA replication checkpoint signaling / Polymerase switching / regulation of phosphorylation / CMG complex / Processive synthesis on the lagging strand / DNA replication preinitiation complex / MCM complex / lagging strand elongation / Removal of the Flap Intermediate / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / Polymerase switching on the C-strand of the telomere / mitotic DNA replication initiation / DNA replication, synthesis of primer / mitotic intra-S DNA damage checkpoint signaling / regulation of DNA-templated DNA replication initiation / inner cell mass cell proliferation / DNA strand elongation involved in DNA replication / Apoptotic cleavage of cellular proteins / branching morphogenesis of an epithelial tube / DNA synthesis involved in DNA repair / positive regulation of double-strand break repair / leading strand elongation / G1/S-Specific Transcription / mitotic G2 DNA damage checkpoint signaling / nuclear replication fork / replication fork processing / DNA replication origin binding / cochlea development / DNA replication initiation / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / response to UV / positive regulation of double-strand break repair via homologous recombination / cellular response to interleukin-4 / DNA helicase activity / lung development / cellular response to epidermal growth factor stimulus / DNA damage checkpoint signaling / morphogenesis of an epithelium / Defective pyroptosis / Assembly of the pre-replicative complex / enzyme activator activity / helicase activity / circadian rhythm / regulation of circadian rhythm / peptidyl-serine phosphorylation / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / multicellular organism growth / cellular response to xenobiotic stimulus / nuclear matrix / Orc1 removal from chromatin / protein import into nucleus / DNA-directed RNA polymerase activity / cellular senescence / nuclear envelope / mitotic cell cycle / nucleosome assembly / single-stranded DNA binding / site of double-strand break / 4 iron, 4 sulfur cluster binding / Processing of DNA double-strand break ends / histone binding / DNA helicase / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / chromosome, telomeric region / DNA replication / cell population proliferation / Ub-specific processing proteases / cilium / ciliary basal body
Similarity search - Function
: / WDHD1 HMG box / WDHD1 first WD40 domain / Claspin / Timeless, C-terminal / Timeless PAB domain / DNA polymerase alpha, subunit B, N-terminal domain superfamily / Chromosome segregation in meiosis protein 3 / TIPIN/Csm3/Swi3 / Replication Fork Protection Component Swi3 ...: / WDHD1 HMG box / WDHD1 first WD40 domain / Claspin / Timeless, C-terminal / Timeless PAB domain / DNA polymerase alpha, subunit B, N-terminal domain superfamily / Chromosome segregation in meiosis protein 3 / TIPIN/Csm3/Swi3 / Replication Fork Protection Component Swi3 / : / DNA polymerase alpha subunit B, OB domain / DNA polymerase alpha subunit B N-terminal / DNA polymerase alpha, subunit B, N-terminal / Timeless, N-terminal / Timeless / Timeless protein / : / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / DNA polymerase alpha, subunit B / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, large subunit, eukaryotic / DNA primase, small subunit / DNA primase small subunit / DNA primase large subunit, eukaryotic/archaeal / DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / Eukaryotic and archaeal DNA primase, large subunit C-terminal domain / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA replication licensing factor MCM2-like, winged-helix domain / DNA polymerase alpha catalytic subunit, catalytic domain / : / PSF2 N-terminal domain / : / : / PSF3 N-terminal domain / PSF1 C-terminal domain / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45 / GINS complex, subunit Psf3 / DNA replication complex GINS protein SLD5, C-terminal / GINS complex, subunit Psf3 superfamily / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / GINS subunit, domain A / GINS complex protein helical bundle domain / GINS complex, subunit Psf1 / GINS, helical bundle-like domain superfamily / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / : / MCM5, C-terminal domain / DNA replication licensing factor MCM7, winged helix / DNA replication licensing factor Mcm5 / MCM4, winged helix domain / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / : / MCM3-like, winged helix domain / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Mcm6, C-terminal winged-helix domain / MCM6 C-terminal winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / DNA polymerase family B, thumb domain / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Cell division control protein 45 homolog / WD repeat and HMG-box DNA-binding protein 1 / DNA polymerase alpha catalytic subunit / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM5 / DNA replication licensing factor MCM7 ...PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Cell division control protein 45 homolog / WD repeat and HMG-box DNA-binding protein 1 / DNA polymerase alpha catalytic subunit / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM5 / DNA replication licensing factor MCM7 / DNA primase small subunit / DNA primase large subunit / DNA replication licensing factor MCM2 / DNA polymerase alpha subunit B / DNA replication licensing factor MCM6 / DNA replication complex GINS protein PSF1 / DNA replication complex GINS protein SLD5 / DNA replication complex GINS protein PSF3 / TIMELESS-interacting protein / Claspin / Protein timeless homolog / DNA replication complex GINS protein PSF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJones, M.L. / Yeeles, J.T.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/12 United Kingdom
CitationJournal: Mol Cell / Year: 2023
Title: How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication.
Authors: Morgan L Jones / Valentina Aria / Yasemin Baris / Joseph T P Yeeles /
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 ...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.
History
DepositionOct 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: DNA replication licensing factor MCM2
3: DNA replication licensing factor MCM3
4: DNA replication licensing factor MCM4
5: DNA replication licensing factor MCM5
6: DNA replication licensing factor MCM6
7: DNA replication licensing factor MCM7
A: DNA polymerase alpha subunit B
C: Cell division control protein 45 homolog
D: DNA replication complex GINS protein PSF1
E: DNA replication complex GINS protein PSF2
F: DNA replication complex GINS protein PSF3
G: DNA replication complex GINS protein SLD5
K: Protein timeless homolog
L: TIMELESS-interacting protein
M: Leading strand DNA
N: DNA Molecule
P: DNA primase large subunit
Q: Claspin
O: DNA primase small subunit
H: WD repeat and HMG-box DNA-binding protein 1
B: DNA polymerase alpha catalytic subunit
J: WD repeat and HMG-box DNA-binding protein 1
I: WD repeat and HMG-box DNA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,834,17733
Polymers1,832,32323
Non-polymers1,85310
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA replication licensing factor ... , 6 types, 6 molecules 234567

#1: Protein DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2 homolog / Nuclear protein BM28


Mass: 102034.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM2, BM28, CCNL1, CDCL1, KIAA0030 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49736, DNA helicase
#2: Protein DNA replication licensing factor MCM3 / DNA polymerase alpha holoenzyme-associated protein P1 / P1-MCM3 / RLF subunit beta / p102


Mass: 91110.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P25205, DNA helicase
#3: Protein DNA replication licensing factor MCM4 / CDC21 homolog / P1-CDC21


Mass: 96684.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM4, CDC21 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P33991, DNA helicase
#4: Protein DNA replication licensing factor MCM5 / CDC46 homolog / P1-CDC46


Mass: 82406.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM5, CDC46 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P33992, DNA helicase
#5: Protein DNA replication licensing factor MCM6 / p105MCM


Mass: 93010.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14566, DNA helicase
#6: Protein DNA replication licensing factor MCM7 / CDC47 homolog / P1.1-MCM3


Mass: 81411.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM7, CDC47, MCM2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P33993, DNA helicase

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DNA polymerase alpha ... , 2 types, 2 molecules AB

#7: Protein DNA polymerase alpha subunit B / DNA polymerase alpha 70 kDa subunit


Mass: 66015.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLA2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14181
#21: Protein DNA polymerase alpha catalytic subunit / DNA polymerase alpha catalytic subunit p180


Mass: 170392.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLA1, POLA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P09884, DNA-directed DNA polymerase

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Protein , 7 types, 9 molecules CKLPQOHJI

#8: Protein Cell division control protein 45 homolog / PORC-PI-1


Mass: 66016.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC45, CDC45L, CDC45L2, UNQ374/PRO710 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75419
#13: Protein Protein timeless homolog / hTIM


Mass: 138903.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMELESS, TIM, TIM1, TIMELESS1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UNS1
#14: Protein TIMELESS-interacting protein


Mass: 34600.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIPIN / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BVW5
#17: Protein DNA primase large subunit / DNA primase 58 kDa subunit / p58


Mass: 58890.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM2, PRIM2A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49643
#18: Protein Claspin / hClaspin


Mass: 155184.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLSPN / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9HAW4
#19: Protein DNA primase small subunit / DNA primase 49 kDa subunit / p49


Mass: 54242.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49642, DNA primase AEP
#20: Protein WD repeat and HMG-box DNA-binding protein 1 / Acidic nucleoplasmic DNA-binding protein 1 / And-1


Mass: 129966.961 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDHD1, AND1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75717

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DNA replication complex GINS protein ... , 4 types, 4 molecules DEFG

#9: Protein DNA replication complex GINS protein PSF1 / GINS complex subunit 1


Mass: 23022.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GINS1, KIAA0186, PSF1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14691
#10: Protein DNA replication complex GINS protein PSF2 / GINS complex subunit 2


Mass: 21453.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GINS2, PSF2, CGI-122, DC5, HSPC037 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y248
#11: Protein DNA replication complex GINS protein PSF3 / GINS complex subunit 3


Mass: 24562.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GINS3, PSF3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BRX5
#12: Protein DNA replication complex GINS protein SLD5 / GINS complex subunit 4


Mass: 29983.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GINS4, SLD5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BRT9

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DNA chain , 2 types, 2 molecules MN

#15: DNA chain Leading strand DNA


Mass: 26092.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#16: DNA chain DNA Molecule


Mass: 26402.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 10 molecules

#22: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#23: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human replisome bound by pol alpha, engaged on a fork DNA substrate with a 60 nucleotide lagging strand.
Type: COMPLEX
Entity ID: #19, #7, #21, #17, #1-#6, #8-#12, #20, #13-#16, #18
Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 37.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20_4459: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174696 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00867574
ELECTRON MICROSCOPYf_angle_d0.99191482
ELECTRON MICROSCOPYf_dihedral_angle_d13.54325739
ELECTRON MICROSCOPYf_chiral_restr0.05510197
ELECTRON MICROSCOPYf_plane_restr0.00911646

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