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- EMDB-48312: Catalytic domain of human DNA polymerase alpha in complex with DN... -

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Basic information

Entry
Database: EMDB / ID: EMD-48312
TitleCatalytic domain of human DNA polymerase alpha in complex with DNA and RPA
Map datacomposite map, 3.5 angstrom
Sample
  • Complex: Ternary complex of DNA polymerase alpha with DNA and replication protein A
    • Protein or peptide: Replication protein A 14 kDa subunit
    • Protein or peptide: Replication protein A 32 kDa subunit
    • Protein or peptide: Replication protein A 70 kDa DNA-binding subunit
    • Other: RNA-DNA primer (11-mer)
    • Protein or peptide: DNA polymerase alpha catalytic subunit
    • DNA: DNA template (35-mer)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
KeywordsDNA replication / Replication-DNA-RNA complex
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of type I interferon production / alpha DNA polymerase:primase complex / Polymerase switching / single-stranded telomeric DNA binding / chromatin-protein adaptor activity ...protein localization to chromosome / DNA replication factor A complex / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of type I interferon production / alpha DNA polymerase:primase complex / Polymerase switching / single-stranded telomeric DNA binding / chromatin-protein adaptor activity / Processive synthesis on the lagging strand / regulation of DNA damage checkpoint / G-rich strand telomeric DNA binding / DNA replication, synthesis of primer / protein localization to site of double-strand break / lagging strand elongation / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / mitotic DNA replication initiation / HDR through Single Strand Annealing (SSA) / regulation of double-strand break repair via homologous recombination / Impaired BRCA2 binding to RAD51 / DNA synthesis involved in DNA repair / DNA strand elongation involved in DNA replication / telomeric DNA binding / leading strand elongation / G1/S-Specific Transcription / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / DNA replication origin binding / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / DNA replication initiation / HSF1 activation / telomere maintenance via telomerase / mismatch repair / SUMOylation of DNA damage response and repair proteins / Activation of ATR in response to replication stress / mitotic G1 DNA damage checkpoint signaling / telomere maintenance / regulation of mitotic cell cycle / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Defective pyroptosis / meiotic cell cycle / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / G2/M DNA damage checkpoint / base-excision repair / PML body / Meiotic recombination / HDR through Homologous Recombination (HRR) / double-strand break repair via nonhomologous end joining / Dual Incision in GG-NER / DNA-templated DNA replication / Formation of Incision Complex in GG-NER / nuclear matrix / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / nuclear envelope / single-stranded DNA binding / regulation of cell population proliferation / site of double-strand break / Processing of DNA double-strand break ends / protein phosphatase binding / DNA recombination / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / chromosome, telomeric region / DNA replication / nuclear body / DNA repair / nucleotide binding / ubiquitin protein ligase binding / DNA damage response / chromatin binding / protein kinase binding / chromatin / nucleolus / enzyme binding / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein 3 / Replication factor A protein 3 / Replication factor-A protein 1, N-terminal domain / Replication factor A protein-like / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain ...Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein 3 / Replication factor A protein 3 / Replication factor-A protein 1, N-terminal domain / Replication factor A protein-like / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / 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 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / 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 polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase alpha catalytic subunit / Replication protein A 32 kDa subunit / Replication protein A 70 kDa DNA-binding subunit / Replication protein A 14 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBaranovskiy AG / Morstadt LM / Romero EE / Babayeva ND / Tahirov TH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM152032 United States
CitationJournal: To Be Published
Title: Human primosome requires replication protein A when copying DNA with inverted repeats
Authors: Baranovskiy AG / Morstadt LM / Romero EE / Babayeva ND / Tahirov TH
History
DepositionDec 13, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48312.png

Downloads & links

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Map

FileDownload / File: emd_48312.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map, 3.5 angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.72 Å/pix.
x 450 pix.
= 324. Å		0.72 Å/pix.
x 450 pix.
= 324. Å		0.72 Å/pix.
x 450 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-21.874872 - 39.672035000000001
Average (Standard dev.)0.0021560192 (±1.0123504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ternary complex of DNA polymerase alpha with DNA and replication ...

EntireName: Ternary complex of DNA polymerase alpha with DNA and replication protein A
Components
  • Complex: Ternary complex of DNA polymerase alpha with DNA and replication protein A
    • Protein or peptide: Replication protein A 14 kDa subunit
    • Protein or peptide: Replication protein A 32 kDa subunit
    • Protein or peptide: Replication protein A 70 kDa DNA-binding subunit
    • Other: RNA-DNA primer (11-mer)
    • Protein or peptide: DNA polymerase alpha catalytic subunit
    • DNA: DNA template (35-mer)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

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Supramolecule #1: Ternary complex of DNA polymerase alpha with DNA and replication ...

SupramoleculeName: Ternary complex of DNA polymerase alpha with DNA and replication protein A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Replication protein A 14 kDa subunit

MacromoleculeName: Replication protein A 14 kDa subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.583714 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MVDMMDLPRS RINAGMLAQF IDKPVCFVGR LEKIHPTGKM FILSDGEGKN GTIELMEPLD EEISGIVEVV GRVTAKATIL CTSYVQFKE DSHPFDLGLY NEAVKIIHDF PQFYPLGIVQ HD

UniProtKB: Replication protein A 14 kDa subunit

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Macromolecule #2: Replication protein A 32 kDa subunit

MacromoleculeName: Replication protein A 32 kDa subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.931359 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AEKKSRARAQ HIVPCTISQL LSATLVDEVF RIGNVEISQV TIVGIIRHAE KAPTNIVYKI DDMTAAPMDV RQWVDTDDTS SENTVVPPE TYVKVAGHLR SFQNKKSLVA FKIMPLEDMN EFTTHILEVI NAHMVLSKAN SQPSAGRAPI SNPGMSEAGN F GGNSFMPA ...String:
AEKKSRARAQ HIVPCTISQL LSATLVDEVF RIGNVEISQV TIVGIIRHAE KAPTNIVYKI DDMTAAPMDV RQWVDTDDTS SENTVVPPE TYVKVAGHLR SFQNKKSLVA FKIMPLEDMN EFTTHILEVI NAHMVLSKAN SQPSAGRAPI SNPGMSEAGN F GGNSFMPA NGLTVAQNQV LNLIKACPRP EGLNFQDLKN QLKHMSVSSI KQAVDFLSNE GHIYSTVDDD HFKSTDAE

UniProtKB: Replication protein A 32 kDa subunit

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Macromolecule #3: Replication protein A 70 kDa DNA-binding subunit

MacromoleculeName: Replication protein A 70 kDa DNA-binding subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.031748 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SNTNWKTLYE VKSENLGQGD KPDYFSSVAT VVYLRKENCM YQACPTQDCN KKVIDQQNGL YRCEKCDTEF PNFKYRMILS VNIADFQEN QWVTCFQESA EAILGQNAAY LGELKDKNEQ AFEEVFQNAN FRSFIFRVRV KVETYNDESR IKATVMDVKP V DYREYGRR LVMSIRRSAL M

UniProtKB: Replication protein A 70 kDa DNA-binding subunit

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Macromolecule #5: DNA polymerase alpha catalytic subunit

MacromoleculeName: DNA polymerase alpha catalytic subunit / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 103.957078 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ADEEQVFHFY WLDAYEDQYN QPGVVFLFGK VWIESAETHV SCCVMVKNIE RTLYFLPREM KIDLNTGKET GTPISMKDVY EEFDEKIAT KYKIMKFKSK PVEKNYAFEI PDVPEKSEYL EVKYSAEMPQ LPQDLKGETF SHVFGTNTSS LELFLMNRKI K GPCWLEVK ...String:
ADEEQVFHFY WLDAYEDQYN QPGVVFLFGK VWIESAETHV SCCVMVKNIE RTLYFLPREM KIDLNTGKET GTPISMKDVY EEFDEKIAT KYKIMKFKSK PVEKNYAFEI PDVPEKSEYL EVKYSAEMPQ LPQDLKGETF SHVFGTNTSS LELFLMNRKI K GPCWLEVK SPQLLNQPVS WCKVEAMALK PDLVNVIKDV SPPPLVVMAF SMKTMQNAKN HQNEIIAMAA LVHHSFALDK AA PKPPFQS HFCVVSKPKD CIFPYAFKEV IEKKNVKVEV AATERTLLGF FLAKVHKIDP DIIVGHNIYG FELEVLLQRI NVC KAPHWS KIGRLKRSNM PKLGGRSGFG ERNATCGRMI CDVEISAKEL IRCKSYHLSE LVQQILKTER VVIPMENIQN MYSE SSQLL YLLEHTWKDA KFILQIMCEL NVLPLALQIT NIAGNIMSRT LMGGRSERNE FLLLHAFYEN NYIVPDKQIF RKPQQ KLGD EDEEIDGDTN KYKKGRKKAA YAGGLVLDPK VGFYDKFILL LDFNSLYPSI IQEFNICFTT VQRVASEAQK VTEDGE QEQ IPELPDPSLE MGILPREIRK LVERRKQVKQ LMKQQDLNPD LILQYDIRQK ALKLTANSMY GCLGFSYSRF YAKPLAA LV TYKGREILMH TKEMVQKMNL EVIYGDTDSI MINTNSTNLE EVFKLGNKVK SEVNKLYKLL EIDIDGVFKS LLLLKKKK Y AALVVEPTSD GNYVTKQELK GLDIVRRDWC DLAKDTGNFV IGQILSDQSR DTIVENIQKR LIEIGENVLN GSVPVSQFE INKALTKDPQ DYPDKKSLPH VHVALWINSQ GGRKVKAGDT VSYVICQDGS NLTASQRAYA PEQLQKQDNL TIDTQYYLAQ QIHPVVARI CEPIDGIDAV LIATWLGLDP T

UniProtKB: DNA polymerase alpha catalytic subunit

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Macromolecule #4: RNA-DNA primer (11-mer)

MacromoleculeName: RNA-DNA primer (11-mer) / type: other / ID: 4 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.50517 KDa
SequenceString:
GCCUGGAGC(DG) (DC)

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Macromolecule #6: DNA template (35-mer)

MacromoleculeName: DNA template (35-mer) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.764963 KDa
SequenceString:
(DA)(DA)(DT)(DC)(DT)(DA)(DG)(DT)(DA)(DA) (DC)(DA)(DT)(DA)(DG)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DA)(DG)(DG)(DC)(DG)(DC)(DT) (DC)(DC)(DA)(DG)(DG)(DC)

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: DCP
Molecular weightTheoretical: 467.157 Da
Chemical component information

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-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

BufferpH: 7.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18529
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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