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- EMDB-13534: Cryo-EM map of the core human replisome on a DNA substrate lackin... -

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Basic information

Entry
Database: EMDB / ID: EMD-13534
TitleCryo-EM map of the core human replisome on a DNA substrate lacking a 5'-flap
Map dataCore human replisome on fork DNA lacking a 5'-flap
Sample
  • Complex: Core human replisome lacking a 5'-flap
Function / homology
Function and homology information


cellular response to bleomycin / DNA secondary structure binding / detection of abiotic stimulus / replication fork arrest / regulation of nuclear cell cycle DNA replication / Switching of origins to a post-replicative state / Unwinding of DNA / cell cycle phase transition / cellular response to cisplatin / DNA replication initiation ...cellular response to bleomycin / DNA secondary structure binding / detection of abiotic stimulus / replication fork arrest / regulation of nuclear cell cycle DNA replication / Switching of origins to a post-replicative state / Unwinding of DNA / cell cycle phase transition / cellular response to cisplatin / DNA replication initiation / epsilon DNA polymerase complex / DNA strand elongation involved in mitotic DNA replication / GINS complex / mitotic DNA replication preinitiation complex assembly / nuclear origin of replication recognition complex / cellular response to hydroxyurea / anaphase-promoting complex binding / cullin-RING-type E3 NEDD8 transferase / alpha DNA polymerase:primase complex / mitotic DNA replication / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / CMG complex / DNA replication checkpoint signaling / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul7-RING ubiquitin ligase complex / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication preinitiation complex / nucleotide-excision repair, DNA gap filling / target-directed miRNA degradation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / regulation of phosphorylation / MCM complex / elongin complex / VCB complex / DNA replication proofreading / mitotic DNA replication checkpoint signaling / replication fork protection complex / positive regulation of protein autoubiquitination / double-strand break repair via break-induced replication / protein neddylation / mitotic DNA replication initiation / mitotic intra-S DNA damage checkpoint signaling / NEDD8 ligase activity / positive regulation of double-strand break repair / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / regulation of DNA-templated DNA replication initiation / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / inner cell mass cell proliferation / ubiquitin-ubiquitin ligase activity / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4B-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / DNA strand elongation involved in DNA replication / branching morphogenesis of an epithelial tube / activation of protein kinase activity / DNA synthesis involved in DNA repair / cochlea development / G1/S-Specific Transcription / DNA unwinding involved in DNA replication / leading strand elongation / Apoptotic cleavage of cellular proteins / replication fork processing / Prolactin receptor signaling / nuclear replication fork / protein monoubiquitination / mitotic G2 DNA damage checkpoint signaling / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cullin family protein binding / DNA replication origin binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of double-strand break repair via homologous recombination / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Tat-mediated elongation of the HIV-1 transcript / DNA replication initiation / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / cellular response to interleukin-4 / Formation of HIV elongation complex in the absence of HIV Tat / protein K48-linked ubiquitination / error-prone translesion synthesis / Nuclear events stimulated by ALK signaling in cancer / Activation of ATR in response to replication stress / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV / RNA Polymerase II Pre-transcription Events / base-excision repair, gap-filling / T cell activation / positive regulation of TORC1 signaling
Similarity search - Function
DNA polymerase epsilon subunit B, N-terminal / DNA polymerases epsilon N terminal / Claspin / Timeless, C-terminal / Timeless PAB domain / GINS/PriA/YqbF domain / Chromosome segregation in meiosis protein 3 / TIPIN/Csm3/Swi3 / Replication Fork Protection Component Swi3 / Timeless ...DNA polymerase epsilon subunit B, N-terminal / DNA polymerases epsilon N terminal / Claspin / Timeless, C-terminal / Timeless PAB domain / GINS/PriA/YqbF domain / Chromosome segregation in meiosis protein 3 / TIPIN/Csm3/Swi3 / Replication Fork Protection Component Swi3 / Timeless / Timeless, N-terminal / Timeless protein / DNA polymerase epsilon, subunit B / : / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / 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 / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45-like protein / GINS complex, subunit Psf1 / GINS complex, subunit Psf3 / GINS complex, subunit Psf3 superfamily / DNA replication complex GINS protein SLD5, C-terminal / GINS, helical bundle-like domain 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 / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / MCM4, winged helix domain / DNA replication licensing factor Mcm5 / 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 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / Cullin protein neddylation domain / MCM N-terminal domain / MCM N-terminal domain / : / Cullin, conserved site / Cullin family signature. / Elongin B / Cullin / Elongin-C / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM OB domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / DNA polymerase family B, thumb domain / HMG boxes A and B DNA-binding domains profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / 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 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / SKP1/BTB/POZ domain superfamily
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 / E3 ubiquitin-protein ligase RBX1 / DNA polymerase epsilon catalytic subunit A ...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 / E3 ubiquitin-protein ligase RBX1 / DNA polymerase epsilon catalytic subunit A / Cullin-2 / DNA replication licensing factor MCM6 / DNA replication complex GINS protein PSF1 / Elongin-C / Elongin-B / Leucine-rich repeat protein 1 / 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: 3.1 Å
AuthorsJones MJ / Yeeles JTP / Jenkyn-Bedford M / Deegan TD
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/12 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_12016/13 United Kingdom
Wellcome Trust204678/Z/16/Z United Kingdom
CitationJournal: Nature / Year: 2021
Title: A conserved mechanism for regulating replisome disassembly in eukaryotes.
Authors: Michael Jenkyn-Bedford / Morgan L Jones / Yasemin Baris / Karim P M Labib / Giuseppe Cannone / Joseph T P Yeeles / Tom D Deegan /
Abstract: Replisome disassembly is the final step of eukaryotic DNA replication and is triggered by ubiquitylation of the CDC45-MCM-GINS (CMG) replicative helicase. Despite being driven by evolutionarily ...Replisome disassembly is the final step of eukaryotic DNA replication and is triggered by ubiquitylation of the CDC45-MCM-GINS (CMG) replicative helicase. Despite being driven by evolutionarily diverse E3 ubiquitin ligases in different eukaryotes (SCF in budding yeast, CUL2 in metazoa), replisome disassembly is governed by a common regulatory principle, in which ubiquitylation of CMG is suppressed before replication termination, to prevent replication fork collapse. Recent evidence suggests that this suppression is mediated by replication fork DNA. However, it is unknown how SCF and CUL2 discriminate terminated from elongating replisomes, to selectively ubiquitylate CMG only after termination. Here we used cryo-electron microscopy to solve high-resolution structures of budding yeast and human replisome-E3 ligase assemblies. Our structures show that the leucine-rich repeat domains of Dia2 and LRR1 are structurally distinct, but bind to a common site on CMG, including the MCM3 and MCM5 zinc-finger domains. The LRR-MCM interaction is essential for replisome disassembly and, crucially, is occluded by the excluded DNA strand at replication forks, establishing the structural basis for the suppression of CMG ubiquitylation before termination. Our results elucidate a conserved mechanism for the regulation of replisome disassembly in eukaryotes, and reveal a previously unanticipated role for DNA in preserving replisome integrity.
History
DepositionSep 2, 2021-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0098
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0098
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13534.png

Downloads & links

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Map

FileDownload / File: emd_13534.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCore human replisome on fork DNA lacking a 5'-flap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 428.8 Å		1.07 Å/pix.
x 400 pix.
= 428.8 Å		1.07 Å/pix.
x 400 pix.
= 428.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0098 / Movie #1: 0.0098
Minimum - Maximum-0.021223396 - 0.06431743
Average (Standard dev.)0.00024358957 (±0.0021321326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 428.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0721.0721.072
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z428.800428.800428.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0210.0640.000

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Supplemental data

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Sample components

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Entire : Core human replisome lacking a 5'-flap

EntireName: Core human replisome lacking a 5'-flap
Components
  • Complex: Core human replisome lacking a 5'-flap

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Supramolecule #1: Core human replisome lacking a 5'-flap

SupramoleculeName: Core human replisome lacking a 5'-flap / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#24
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: 7.6
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 16721 / Average exposure time: 4.0 sec. / Average electron dose: 38.8 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: 2.8000000000000003 µm / Nominal defocus min: 0.8 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: 2412000
CTF correctionSoftware - Name: RELION (ver. 3)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 350000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2)

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