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- EMDB-27258: Human DNA polymerase-alpha/primase elongation complex II bound to... -

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Basic information

Entry
Database: EMDB / ID: EMD-27258
TitleHuman DNA polymerase-alpha/primase elongation complex II bound to primer/template
Map dataUnsharpened and flipped map
Sample
  • Complex: Elongation complex II of human DNA polymerase alpha/primase bound to RNA-DNA primer and DNA template
    • Protein or peptide: DNA primase small subunitPrimase
    • Protein or peptide: DNA primase large subunitPrimase
    • Protein or peptide: DNA polymerase alpha catalytic subunit
    • Protein or peptide: DNA polymerase alpha subunit BDNA polymerase
    • Other: DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3')
    • DNA: DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3')
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: MAGNESIUM ION
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
KeywordsDNA replication / human DNA polymerase alpha/primase / human primosome / elongation complex / REPLICATION
Function / homology
Function and homology information


DNA primase AEP / positive regulation of DNA primase activity / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex ...DNA primase AEP / positive regulation of DNA primase activity / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / regulation of type I interferon production / Removal of the Flap Intermediate / DNA primase activity / Polymerase switching on the C-strand of the telomere / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / leading strand elongation / DNA synthesis involved in DNA repair / G1/S-Specific Transcription / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex / Defective pyroptosis / nuclear matrix / double-strand break repair via nonhomologous end joining / protein import into nucleus / single-stranded DNA binding / nuclear envelope / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA repair / chromatin binding / chromatin / nucleolus / protein kinase binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm / membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
DNA polymerase alpha, subunit B, N-terminal domain superfamily / DNA polymerase alpha subunit B N-terminal / DNA polymerase alpha, subunit B, N-terminal / DNA polymerase alpha, subunit B / 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, subunit B, N-terminal domain superfamily / DNA polymerase alpha subunit B N-terminal / DNA polymerase alpha, subunit B, N-terminal / DNA polymerase alpha, subunit B / 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 / 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 alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / 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 / DNA primase small subunit / DNA primase large subunit / DNA polymerase alpha subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsHe Q / Baranovskiy A / Lim C / Tahirov T
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM131023 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127085 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structures of human primosome elongation complexes.
Authors: Qixiang He / Andrey G Baranovskiy / Lucia M Morstadt / Alisa E Lisova / Nigar D Babayeva / Benjamin L Lusk / Ci Ji Lim / Tahir H Tahirov /
Abstract: The synthesis of RNA-DNA primer by primosome requires coordination between primase and DNA polymerase α subunits, which is accompanied by unknown architectural rearrangements of multiple domains. ...The synthesis of RNA-DNA primer by primosome requires coordination between primase and DNA polymerase α subunits, which is accompanied by unknown architectural rearrangements of multiple domains. Using cryogenic electron microscopy, we solved a 3.6 Å human primosome structure caught at an early stage of RNA primer elongation with deoxynucleotides. The structure confirms a long-standing role of primase large subunit and reveals new insights into how primosome is limited to synthesizing short RNA-DNA primers.
History
DepositionJun 9, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateMay 31, 2023-
Current statusMay 31, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27258.png

Downloads & links

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Map

FileDownload / File: emd_27258.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened and flipped map
Voxel sizeX=Y=Z: 1.12 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.23665486 - 0.9218383
Average (Standard dev.)0.0020708314 (±0.023099817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 286.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_27258_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_27258_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Elongation complex II of human DNA polymerase alpha/primase bound...

EntireName: Elongation complex II of human DNA polymerase alpha/primase bound to RNA-DNA primer and DNA template
Components
  • Complex: Elongation complex II of human DNA polymerase alpha/primase bound to RNA-DNA primer and DNA template
    • Protein or peptide: DNA primase small subunitPrimase
    • Protein or peptide: DNA primase large subunitPrimase
    • Protein or peptide: DNA polymerase alpha catalytic subunit
    • Protein or peptide: DNA polymerase alpha subunit BDNA polymerase
    • Other: DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3')
    • DNA: DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3')
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: MAGNESIUM ION
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

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Supramolecule #1: Elongation complex II of human DNA polymerase alpha/primase bound...

SupramoleculeName: Elongation complex II of human DNA polymerase alpha/primase bound to RNA-DNA primer and DNA template
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: Larger elongation complex solved using cryo-EM single-particle analysis
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 340 KDa

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Macromolecule #1: DNA primase small subunit

MacromoleculeName: DNA primase small subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA primase AEP
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.981012 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: METFDPTELP ELLKLYYRRL FPYSQYYRWL NYGGVIKNYF QHREFSFTLK DDIYIRYQSF NNQSDLEKEM QKMNPYKIDI GAVYSHRPN QHNTVKLGAF QAQEKELVFD IDMTDYDDVR RCCSSADICP KCWTLMTMAI RIIDRALKED FGFKHRLWVY S GRRGVHCW ...String:
METFDPTELP ELLKLYYRRL FPYSQYYRWL NYGGVIKNYF QHREFSFTLK DDIYIRYQSF NNQSDLEKEM QKMNPYKIDI GAVYSHRPN QHNTVKLGAF QAQEKELVFD IDMTDYDDVR RCCSSADICP KCWTLMTMAI RIIDRALKED FGFKHRLWVY S GRRGVHCW VCDESVRKLS SAVRSGIVEY LSLVKGGQDV KKKVHLSEKI HPFIRKSINI IKKYFEEYAL VNQDILENKE SW DKILALV PETIHDELQQ SFQKSHNSLQ RWEHLKKVAS RYQNNIKNDK YGPWLEWEIM LQYCFPRLDI NVSKGINHLL KSP FSVHPK TGRISVPIDL QKVDQFDPFT VPTISFICRE LDAISTNEEE KEENEAESDV KHRTRDYKKT SLAPYVKVFE HFLE NLDKS RKGELLKKSD LQKDF

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Macromolecule #2: DNA primase large subunit

MacromoleculeName: DNA primase large subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.890918 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MEFSGRKWRK LRLAGDQRNA SYPHCLQFYL QPPSENISLI EFENLAIDRV KLLKSVENLG VSYVKGTEQY QSKLESELRK LKFSYRENL EDEYEPRRRD HISHFILRLA YCQSEELRRW FIQQEMDLLR FRFSILPKDK IQDFLKDSQL QFEAISDEEK T LREQEIVA ...String:
MEFSGRKWRK LRLAGDQRNA SYPHCLQFYL QPPSENISLI EFENLAIDRV KLLKSVENLG VSYVKGTEQY QSKLESELRK LKFSYRENL EDEYEPRRRD HISHFILRLA YCQSEELRRW FIQQEMDLLR FRFSILPKDK IQDFLKDSQL QFEAISDEEK T LREQEIVA SSPSLSGLKL GFESIYKIPF ADALDLFRGR KVYLEDGFAY VPLKDIVAII LNEFRAKLSK ALALTARSLP AV QSDERLQ PLLNHLSHSY TGQDYSTQGN VGKISLDQID LLSTKSFPPC MRQLHKALRE NHHLRHGGRM QYGLFLKGIG LTL EQALQF WKQEFIKGKM DPDKFDKGYS YNIRHSFGKE GKRTDYTPFS CLKIILSNPP SQGDYHGCPF RHSDPELLKQ KLQS YKISP GGISQILDLV KGTHYQVACQ KYFEMIHNVD DCGFSLNHPN QFFCESQRIL NGGKDIKKEP IQPETPQPKP SVQKT KDAS SALASLNSSL EMDMEGLEDY FSEDS

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Macromolecule #3: DNA polymerase alpha catalytic subunit

MacromoleculeName: DNA polymerase alpha catalytic subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 166.131094 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAPVHGDDSL SDSGSFVSSR ARREKKSKKG RQEALERLKK AKAGEKYKYE VEDFTGVYEE VDEEQYSKLV QARQDDDWIV DDDGIGYVE DGREIFDDDL EDDALDADEK GKDGKARNKD KRNVKKLAVT KPNNIKSMFI ACAGKKTADK AVDLSKDGLL G DILQDLNT ...String:
MAPVHGDDSL SDSGSFVSSR ARREKKSKKG RQEALERLKK AKAGEKYKYE VEDFTGVYEE VDEEQYSKLV QARQDDDWIV DDDGIGYVE DGREIFDDDL EDDALDADEK GKDGKARNKD KRNVKKLAVT KPNNIKSMFI ACAGKKTADK AVDLSKDGLL G DILQDLNT ETPQITPPPV MILKKKRSIG ASPNPFSVHT ATAVPSGKIA SPVSRKEPPL TPVPLKRAEF AGDDVQVEST EE EQESGAM EFEDGDFDEP MEVEEVDLEP MAAKAWDKES EPAEEVKQEA DSGKGTVSYL GSFLPDVSCW DIDQEGDSSF SVQ EVQVDS SHLPLVKGAD EEQVFHFYWL DAYEDQYNQP GVVFLFGKVW IESAETHVSC CVMVKNIERT LYFLPREMKI DLNT GKETG TPISMKDVYE EFDEKIATKY KIMKFKSKPV EKNYAFEIPD VPEKSEYLEV KYSAEMPQLP QDLKGETFSH VFGTN TSSL ELFLMNRKIK GPCWLEVKSP QLLNQPVSWC KVEAMALKPD LVNVIKDVSP PPLVVMAFSM KTMQNAKNHQ NEIIAM AAL VHHSFALDKA APKPPFQSHF CVVSKPKDCI FPYAFKEVIE KKNVKVEVAA TERTLLGFFL AKVHKIDPDI IVGHNIY GF ELEVLLQRIN VCKAPHWSKI GRLKRSNMPK LGGRSGFGER NATCGRMICD VEISAKELIR CKSYHLSELV QQILKTER V VIPMENIQNM YSESSQLLYL LEHTWKDAKF ILQIMCELNV LPLALQITNI AGNIMSRTLM GGRSERNEFL LLHAFYENN YIVPDKQIFR KPQQKLGDED EEIDGDTNKY KKGRKKAAYA GGLVLDPKVG FYDKFILLLD FNSLYPSIIQ EFNICFTTVQ RVASEAQKV TEDGEQEQIP ELPDPSLEMG ILPREIRKLV ERRKQVKQLM KQQDLNPDLI LQYDIRQKAL KLTANSMYGC L GFSYSRFY AKPLAALVTY KGREILMHTK EMVQKMNLEV IYGDTDSIMI NTNSTNLEEV FKLGNKVKSE VNKLYKLLEI DI DGVFKSL LLLKKKKYAA LVVEPTSDGN YVTKQELKGL DIVRRDWCDL AKDTGNFVIG QILSDQSRDT IVENIQKRLI EIG ENVLNG SVPVSQFEIN KALTKDPQDY PDKKSLPHVH VALWINSQGG RKVKAGDTVS YVICQDGSNL TASQRAYAPE QLQK QDNLT IDTQYYLAQQ IHPVVARICE PIDGIDAVLI ATWLGLDPTQ FRVHHYHKDE ENDALLGGPA QLTDEEKYRD CERFK CPCP TCGTENIYDN VFDGSGTDME PSLYRCSNID CKASPLTFTV QLSNKLIMDI RRFIKKYYDG WLICEEPTCR NRTRHL PLQ FSRTGPLCPA CMKATLQPEY SDKSLYTQLC FYRYIFDAEC ALEKLTTDHE KDKLKKQFFT PKVLQDYRKL KNTAEQF LS RSGYSEVNLS KLFAGCAVKS

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Macromolecule #4: DNA polymerase alpha subunit B

MacromoleculeName: DNA polymerase alpha subunit B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.07459 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ATPSQKYNSR SNRGEVVTSF GLAQGVSWSG RGGAGNISLK VLGCPEALTG SYKSMFQKLP DIREVLTCKI EELGSELKEH YKIEAFTPL LAPAQEPVTL LGQIGCDSNG KLNNKSVILE GDREHSSGAQ IPVDLSELKE YSLFPGQVVI MEGINTTGRK L VATKLYEG ...String:
ATPSQKYNSR SNRGEVVTSF GLAQGVSWSG RGGAGNISLK VLGCPEALTG SYKSMFQKLP DIREVLTCKI EELGSELKEH YKIEAFTPL LAPAQEPVTL LGQIGCDSNG KLNNKSVILE GDREHSSGAQ IPVDLSELKE YSLFPGQVVI MEGINTTGRK L VATKLYEG VPLPFYQPTE EDADFEQSMV LVACGPYTTS DSITYDPLLD LIAVINHDRP DVCILFGPFL DAKHEQVENC LL TSPFEDI FKQCLRTIIE GTRSSGSHLV FVPSLRDVHH EPVYPQPPFS YSDLSREDKK QVQFVSEPCS LSINGVIFGL TST DLLFHL GAEEISSSSG TSDRFSRILK HILTQRSYYP LYPPQEDMAI DYESFYVYAQ LPVTPDVLII PSELRYFVKD VLGC VCVNP GRLTKGQVGG TFARLYLRRP AADGAERQSP CIAVQVVRI

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Macromolecule #5: DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3')

MacromoleculeName: DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3')
type: other / ID: 5 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.977352 KDa
SequenceString:
(GTP)GCGGCACG(DA) (DC)(DC)

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Macromolecule #6: DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*...

MacromoleculeName: DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3')
type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.829786 KDa
SequenceString:
(DA)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DG)(DC) (DC)(DG)(DC)(DC)(DA)(DA)(DT)(DA)(DA)

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 8 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: DTP
Molecular weightTheoretical: 491.182 Da
Chemical component information

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate

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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

Concentration6 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMTRIS-HClTrisTris buffer pH 7.7
100.0 mMKClPotassium Chloride
1.0 mMTCEPTCEP
4.0 mMCHAPSOCHAPS detergentCHAPSOCHAPS detergent
1.0 percentGlycerolGlycerol

Details: CHAPSO is made fresh at 80 mM before added to the sample at a final concentration of 4-8 mM immediately before vitrification.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 13243 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2522283
Startup modelType of model: INSILICO MODEL / In silico model: From cryosparc
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 199286
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4qcl


5f0q


5exr

chain_id: A

5exr

chain_id: D
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8d9d:
Human DNA polymerase-alpha/primase elongation complex II bound to primer/template

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