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- EMDB-13377: Pol-Epsilon/CDC45/GINS multibody refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-13377
TitlePol-Epsilon/CDC45/GINS multibody refinement
Map dataFULL
Sample
  • Complex: Pol epsilon-CDC45-GINS core human replisome multibody refinement
Function / homology
Function and homology information


cellular response to bleomycin / DNA secondary structure 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 / epsilon DNA polymerase complex ...cellular response to bleomycin / DNA secondary structure 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 / epsilon DNA polymerase complex / DNA strand elongation involved in mitotic DNA replication / GINS complex / mitotic DNA replication preinitiation complex assembly / cellular response to cisplatin / cellular response to hydroxyurea / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / anaphase-promoting complex binding / alpha DNA polymerase:primase complex / activation of protein kinase activity / nucleotide-excision repair, DNA gap filling / mitotic DNA replication / DNA replication checkpoint signaling / CMG complex / regulation of phosphorylation / DNA replication proofreading / DNA replication preinitiation complex / single-stranded DNA 3'-5' DNA exonuclease activity / MCM complex / replication fork protection complex / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / mitotic DNA replication initiation / mitotic intra-S DNA damage checkpoint signaling / regulation of DNA-templated DNA replication initiation / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / inner cell mass cell proliferation / positive regulation of double-strand break repair / branching morphogenesis of an epithelial tube / DNA synthesis involved in DNA repair / DNA strand elongation involved in DNA replication / cochlea development / Apoptotic cleavage of cellular proteins / leading strand elongation / G1/S-Specific Transcription / mitotic G2 DNA damage checkpoint signaling / replication fork processing / nuclear replication fork / DNA replication origin binding / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / DNA replication initiation / embryonic organ development / error-prone translesion synthesis / positive regulation of double-strand break repair via homologous recombination / Activation of ATR in response to replication stress / response to UV / base-excision repair, gap-filling / cellular response to epidermal growth factor stimulus / cellular response to interleukin-4 / enzyme activator activity / DNA damage checkpoint signaling / Gap-filling DNA repair synthesis and ligation in GG-NER / morphogenesis of an epithelium / Assembly of the pre-replicative complex / lung development / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / multicellular organism growth / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / G1/S transition of mitotic cell cycle / circadian rhythm / Orc1 removal from chromatin / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular senescence / cellular response to xenobiotic stimulus / nucleosome assembly / mitotic cell cycle / single-stranded DNA binding / peptidyl-serine phosphorylation / site of double-strand break / Processing of DNA double-strand break ends / 4 iron, 4 sulfur cluster binding / DNA helicase / histone binding / DNA-directed DNA polymerase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA-directed DNA polymerase activity / chromosome, telomeric region / cell population proliferation / DNA replication / Ub-specific processing proteases / nuclear body
Similarity search - Function
DNA polymerase epsilon subunit B, N-terminal / DNA polymerases epsilon N terminal / : / WDHD1 HMG box / WDHD1 first WD40 domain / Claspin / Timeless, C-terminal / Timeless PAB domain / Chromosome segregation in meiosis protein 3 / TIPIN/Csm3/Swi3 ...DNA polymerase epsilon subunit B, N-terminal / DNA polymerases epsilon N terminal / : / WDHD1 HMG box / WDHD1 first WD40 domain / Claspin / Timeless, C-terminal / Timeless PAB domain / Chromosome segregation in meiosis protein 3 / TIPIN/Csm3/Swi3 / Replication Fork Protection Component Swi3 / Zinc finger domain of DNA polymerase-epsilon / DNA polymerase epsilon, subunit B / Timeless, N-terminal / Timeless / Timeless protein / : / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / DNA replication licensing factor MCM2-like, winged-helix domain / : / : / DNA polymerase epsilon catalytic subunit A, thumb domain / Zinc finger domain of DNA polymerase-epsilon / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / : / PSF3 N-terminal domain / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45 / GINS complex, subunit Psf1 / GINS complex, subunit Psf3 / DNA replication complex GINS protein SLD5, C-terminal / GINS, helical bundle-like domain superfamily / 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 / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / : / MCM5, C-terminal domain / DNA replication licensing factor Mcm5 / MCM3-like, winged helix domain / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / 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 / HMG boxes A and B DNA-binding domains profile. / DNA polymerase family B, thumb domain / high mobility group / High mobility group box domain / High mobility group box domain superfamily / 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 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cell division control protein 45 homolog / WD repeat and HMG-box DNA-binding protein 1 / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM5 / DNA replication licensing factor MCM7 / DNA replication licensing factor MCM2 / DNA polymerase epsilon subunit 2 / DNA polymerase epsilon catalytic subunit A / DNA replication licensing factor MCM6 ...Cell division control protein 45 homolog / WD repeat and HMG-box DNA-binding protein 1 / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM5 / DNA replication licensing factor MCM7 / DNA replication licensing factor MCM2 / DNA polymerase epsilon subunit 2 / DNA polymerase epsilon catalytic subunit A / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsJones MJ / Yeeles JTP
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: EMBO J / Year: 2021
Title: Structure of a human replisome shows the organisation and interactions of a DNA replication machine.
Authors: Morgan L Jones / Yasemin Baris / Martin R G Taylor / Joseph T P Yeeles /
Abstract: The human replisome is an elaborate arrangement of molecular machines responsible for accurate chromosome replication. At its heart is the CDC45-MCM-GINS (CMG) helicase, which, in addition to ...The human replisome is an elaborate arrangement of molecular machines responsible for accurate chromosome replication. At its heart is the CDC45-MCM-GINS (CMG) helicase, which, in addition to unwinding the parental DNA duplex, arranges many proteins including the leading-strand polymerase Pol ε, together with TIMELESS-TIPIN, CLASPIN and AND-1 that have key and varied roles in maintaining smooth replisome progression. How these proteins are coordinated in the human replisome is poorly understood. We have determined a 3.2 Å cryo-EM structure of a human replisome comprising CMG, Pol ε, TIMELESS-TIPIN, CLASPIN and AND-1 bound to replication fork DNA. The structure permits a detailed understanding of how AND-1, TIMELESS-TIPIN and Pol ε engage CMG, reveals how CLASPIN binds to multiple replisome components and identifies the position of the Pol ε catalytic domain. Furthermore, the intricate network of contacts contributed by MCM subunits and TIMELESS-TIPIN with replication fork DNA suggests a mechanism for strand separation.
History
DepositionAug 11, 2021-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateNov 10, 2021-
Current statusNov 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0144
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0144
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13377.png

Downloads & links

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Map

FileDownload / File: emd_13377.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFULL
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 440 pix.
= 470.8 Å		1.07 Å/pix.
x 440 pix.
= 470.8 Å		1.07 Å/pix.
x 440 pix.
= 470.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0144 / Movie #1: 0.0144
Minimum - Maximum-0.014644294 - 0.05595652
Average (Standard dev.)-0.00014602134 (±0.0015005328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 470.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z470.800470.800470.800
α/β/γ90.00090.00090.000
start NX/NY/NZ7810892
NX/NY/NZ127111124
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0150.056-0.000

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Supplemental data

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Mask #1

Fileemd_13377_msk_1.map
Projections & Slices
AxesZYX

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Half map: HALF 2

Fileemd_13377_half_map_1.map
AnnotationHALF 2
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Half map: HALF 1

Fileemd_13377_half_map_2.map
AnnotationHALF 1
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Sample components

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Entire : Pol epsilon-CDC45-GINS core human replisome multibody refinement

EntireName: Pol epsilon-CDC45-GINS core human replisome multibody refinement
Components
  • Complex: Pol epsilon-CDC45-GINS core human replisome multibody refinement

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Supramolecule #1: Pol epsilon-CDC45-GINS core human replisome multibody refinement

SupramoleculeName: Pol epsilon-CDC45-GINS core human replisome multibody refinement
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 39.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 490000
CTF correctionSoftware - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 110000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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