[English] 日本語
Yorodumi
- EMDB-42142: Complete DNA termination subcomplex 2 of Xenopus laevis DNA polym... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42142
TitleComplete DNA termination subcomplex 2 of Xenopus laevis DNA polymerase alpha-primase
Map dataComplete DNA termination subcomplex 2 of Xenopus laevis DNA polymerase alpha-primase
Sample
  • Complex: Polymerase alpha-primase with a DNA termination substrate
    • Complex: Polymerase alpha
      • Protein or peptide: DNA polymerase alpha catalytic subunit
    • Complex: Primase
    • Complex: DNA termination substrate
      • DNA: DNA template
      • Other: RNA-DNA/DNA primer
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsPrimase / DNA polymerase / chimeric RNA-DNA primer / RNA/DNA hybrid / DNA replication / DNA synthesis / REPLICATION / TRANSFERASE-DNA-RNA complex
Function / homology
Function and homology information


alpha DNA polymerase:primase complex / lagging strand elongation / mitotic DNA replication initiation / DNA replication, synthesis of primer / DNA strand elongation involved in DNA replication / leading strand elongation / DNA replication initiation / nuclear matrix / double-strand break repair via nonhomologous end joining / nuclear envelope ...alpha DNA polymerase:primase complex / lagging strand elongation / mitotic DNA replication initiation / DNA replication, synthesis of primer / DNA strand elongation involved in DNA replication / leading strand elongation / DNA replication initiation / nuclear matrix / double-strand break repair via nonhomologous end joining / nuclear envelope / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin binding / chromatin / nucleolus / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B ...DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase alpha catalytic subunit
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsMullins EA / Chazin WC / Eichman BF
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136401 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118089 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA92584 United States
CitationJournal: bioRxiv / Year: 2023
Title: A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase.
Authors: Elwood A Mullins / Lauren E Salay / Clarissa L Durie / Noah P Bradley / Jane E Jackman / Melanie D Ohi / Walter J Chazin / Brandt F Eichman
Abstract: The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is ...The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5'-end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer/template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase.
History
DepositionSep 27, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42142.png

Downloads & links

-
Map

FileDownload / File: emd_42142.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplete DNA termination subcomplex 2 of Xenopus laevis DNA polymerase alpha-primase
Voxel sizeX=Y=Z: 1.09333 Å
Density
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.013214775 - 0.05580045
Average (Standard dev.)-0.00001966463 (±0.0015995157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 327.9999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Complete DNA termination subcomplex 2 of Xenopus laevis...

Fileemd_42142_additional_1.map
AnnotationComplete DNA termination subcomplex 2 of Xenopus laevis DNA polymerase alpha-primase (locally sharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Complete DNA termination subcomplex 2 of Xenopus laevis...

Fileemd_42142_half_map_1.map
AnnotationComplete DNA termination subcomplex 2 of Xenopus laevis DNA polymerase alpha-primase (half 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Complete DNA termination subcomplex 2 of Xenopus laevis...

Fileemd_42142_half_map_2.map
AnnotationComplete DNA termination subcomplex 2 of Xenopus laevis DNA polymerase alpha-primase (half 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Polymerase alpha-primase with a DNA termination substrate

EntireName: Polymerase alpha-primase with a DNA termination substrate
Components
  • Complex: Polymerase alpha-primase with a DNA termination substrate
    • Complex: Polymerase alpha
      • Protein or peptide: DNA polymerase alpha catalytic subunit
    • Complex: Primase
    • Complex: DNA termination substrate
      • DNA: DNA template
      • Other: RNA-DNA/DNA primer
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Polymerase alpha-primase with a DNA termination substrate

SupramoleculeName: Polymerase alpha-primase with a DNA termination substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Heterotetrameric protein complex with an RNA-DNA/DNA duplex
Molecular weightTheoretical: 330 KDa

-
Supramolecule #2: Polymerase alpha

SupramoleculeName: Polymerase alpha / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Heterodimer consisting of POLA1 and POLA2
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 200 KDa

-
Supramolecule #3: Primase

SupramoleculeName: Primase / type: complex / ID: 3 / Parent: 1 / Details: Heterodimer consisting of PRIM1 and PRIM2
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 110 KDa

-
Supramolecule #4: DNA termination substrate

SupramoleculeName: DNA termination substrate / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2-#3 / Details: RNA-DNA/DNA duplex
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 30 KDa

-
Macromolecule #1: DNA polymerase alpha catalytic subunit

MacromoleculeName: DNA polymerase alpha catalytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 129.009414 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SNAADGSQVF RFYWLDAYED QYSQPGVVYL FGKVWIESAD AYVSCCVSVK NIERTVYLLP RENRVQLSTG KDTGAPVSMM HVYQEFNEA VAEKYKIMKF KSKKVDKDYA FEIPDVPASS EYLEVRYSAD SPQLPQDLKG ETFSHVFGTN TSSLELFLLS R KIKGPSWL ...String:
SNAADGSQVF RFYWLDAYED QYSQPGVVYL FGKVWIESAD AYVSCCVSVK NIERTVYLLP RENRVQLSTG KDTGAPVSMM HVYQEFNEA VAEKYKIMKF KSKKVDKDYA FEIPDVPASS EYLEVRYSAD SPQLPQDLKG ETFSHVFGTN TSSLELFLLS R KIKGPSWL EIKSPQLSSQ PMSWCKVEAV VTRPDQVSVV KDLAPPPVVV LSLSMKTVQN AKTHQNEIVA IAALVHHTFP LD KAPPQPP FQTHFCVLSK LNDCIFPYDY NEAVKQKNAN IEIALTERTL LGFFLAKIHK IDPDVIVGHD IYGFDLEVLL QRI NSCKVP FWSKIGRLRR SVMPKLGGRS GFAERNAACG RIICDIEISA KELIRCKSYH LSELVHQILK AERVVIPPEN IRNA YNDSV HLLYMLENTW IDAKFILQIM CELNVLPLAL QITNIAGNVM SRTLMGGRSE RNEYLLLHAF TENNFIVPDK PVFKK MQQT TVEDNDDMGT DQNKNKSRKK AAYAGGLVLE PKVGFYDKFI LLLDFNSLYP SIIQEYNICF TTVHREAPST QKGEDQ DEI PELPHSDLEM GILPREIRKL VERRRHVKQL MKQPDLNPDL YLQYDIRQKA LKLTANSMYG CLGFSYSRFY AKPLAAL VT HQGREILLHT KEMVQKMNLE VIYGDTDSIM INTNCNNLEE VFKLGNRVKS EINKSYKLLE IDIDGIFKSL LLLKKKKY A ALTVEPTGDG KYVTKQELKG LDIVRRDWCE LAKQAGNYVI SQILSDQPRD SIVENIQKKL TEIGENVTNG TVPITQYEI NKALTKDPQD YPDKKSLPHV HVALWINSQG GRKVKAGDTI SYVICQDGSN LSASQRAYAQ EQLQKQENLS IDTQYYLSQQ VHPVVARIC EPIDGIDSAL IAMWLGLDPS QFRAHRHYQQ DEENDALLGG PSQLTDEEKY RDCERFKFFC PKCGTENIYD N VFDGSGLQ IEPGLKRCSK PECDASPLDY VIQVHNKLLL DIRRYIKKYY SGWLVCEEKT CQNRTRRLPL SFSRNGPICQ AC SKATLRS EYPEKALYTQ LCFYRFIFDW DYALEKVVSE QERGHLKKKL FQESENQYKK LKSTVDQVLS RSGYSEVNLS KLF QTLNTI K

UniProtKB: DNA polymerase alpha catalytic subunit

-
Macromolecule #2: DNA template

MacromoleculeName: DNA template / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.203668 KDa
SequenceString: (DT)(DG)(DT)(DA)(DT)(DG)(DT)(DA)(DT)(DG) (DT)(DA)(DT)(DG)(DT)(DC)(DG)(DC)(DT)(DA) (DC)(DA)(DA)(DT)(DC)(DG)(DC)(DT)(DA) (DA)(DG)(DT)(DT)(DC)(DA)(DC)(DG)(DC)(DA) (DG) (DT)(DA)(DT)(DC)(DC)(DT) ...String:
(DT)(DG)(DT)(DA)(DT)(DG)(DT)(DA)(DT)(DG) (DT)(DA)(DT)(DG)(DT)(DC)(DG)(DC)(DT)(DA) (DC)(DA)(DA)(DT)(DC)(DG)(DC)(DT)(DA) (DA)(DG)(DT)(DT)(DC)(DA)(DC)(DG)(DC)(DA) (DG) (DT)(DA)(DT)(DC)(DC)(DT)(DG)(DT) (DA)(DT)(DG)(DT)(DA)(DT)(DG)(DT)(DA)(DT) (DG)

-
Macromolecule #3: RNA-DNA/DNA primer

MacromoleculeName: RNA-DNA/DNA primer / type: other / ID: 3 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.249697 KDa
SequenceString:
(GTP)GAUACUGC(DG) (DT)(DG)(DA)(DA)(DC)(DT)(DT)(DA)(DG)(DC) (DG)(DA)(DT)(DT)(DG) (DT)(DA)(DG)(DOC)

-
Macromolecule #4: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: DGT
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.9 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 22893 / Average electron dose: 55.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 25216892
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 62414
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

8ucu

source_name: PDB, initial_model_type: experimental model

8g9o

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8ucw:
Complete DNA termination subcomplex 2 of Xenopus laevis DNA polymerase alpha-primase

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more