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- EMDB-53227: YerA41 family-A DNA polymerase in complex with a DNA duplex -

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Basic information

Entry
Database: EMDB / ID: EMD-53227
TitleYerA41 family-A DNA polymerase in complex with a DNA duplex
Map data
Sample
  • Complex: DNA polymerase from YerA41 in complex with dsDNA
    • DNA: DNA (25-MER)
    • DNA: DNA (29-MER)
  • Protein or peptide: DNA polymerase
  • Ligand: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsDNA replication / family-A DNA polymerase / glycosylase / DNA BINDING PROTEIN
Function / homology
Function and homology information


viral DNA genome replication / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesYersinia phage YerA41 (virus) / Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsMissoury S / Delarue M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: YerA41 family-A DNA polymerase in complex with a DNA duplex
Authors: Missoury S / Delarue M
History
DepositionMar 21, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53227.png

Downloads & links

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Map

FileDownload / File: emd_53227.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 288 pix.
= 328.32 Å		1.14 Å/pix.
x 288 pix.
= 328.32 Å		1.14 Å/pix.
x 288 pix.
= 328.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.65039045 - 1.0506256
Average (Standard dev.)-0.00062307506 (±0.02086807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 328.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53227_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53227_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DNA polymerase from YerA41 in complex with dsDNA

EntireName: DNA polymerase from YerA41 in complex with dsDNA
Components
  • Complex: DNA polymerase from YerA41 in complex with dsDNA
    • DNA: DNA (25-MER)
    • DNA: DNA (29-MER)
  • Protein or peptide: DNA polymerase
  • Ligand: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: DNA polymerase from YerA41 in complex with dsDNA

SupramoleculeName: DNA polymerase from YerA41 in complex with dsDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3
Source (natural)Organism: Yersinia phage YerA41 (virus)

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Macromolecule #1: DNA polymerase

MacromoleculeName: DNA polymerase / type: protein_or_peptide / ID: 1 / Details: no density from 90 to 140 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Molecular weightTheoretical: 152.801812 KDa
Recombinant expressionOrganism: Yersinia phage YerA41 (virus)
SequenceString: MSTVLIGYVN IRPGKGGKLI NQDVWKYFEK YVPAHFEDVD LLLFNPQTLP NLSDMIEDLN KYDNIIVTGR EPLKYLGLED AEIDRHSQF SNDDLADDQE EEEEVEDTDN EEDDDSEDDE SGEESDGDDD DDDEFKVKKT KKSDNKIEVM RYFGLINNNP A LKFNKIHV ...String:
MSTVLIGYVN IRPGKGGKLI NQDVWKYFEK YVPAHFEDVD LLLFNPQTLP NLSDMIEDLN KYDNIIVTGR EPLKYLGLED AEIDRHSQF SNDDLADDQE EEEEVEDTDN EEDDDSEDDE SGEESDGDDD DDDEFKVKKT KKSDNKIEVM RYFGLINNNP A LKFNKIHV MYSLMMYIAK DKINVFHFDL LNRTGKNNLV PPMVQIDPKF HHISELESIY HSKWQPDEHK GFAFATRNFP FE PRFRLLG FSLANDTYQA YFYFSRDDDK YAQEMEQYRS VMVKIFLEDA KKLHTYNNKF ENNAVLDQLR ERIFFEDSRI YTQ MLKTRG SLKFSANLFL GVPVWNEGIN TFMKNYKEFV AWMKDYRELS MIEESVIDKN AYEITSIKDL LSSDDKSTLI KLLG LTETD KVKDRSRLEF KLTDDGDKKE PTYKLTTYVV ETYFDLLLDP IKFVEKAMEH SQKYEQSFFK FFMTYQDRLE GKFKL TNLL TYFIKNYNEW QSCGIGDMGY YCILDGYYTV KLKEMLYDTN YDGCADGYIY YLYQSHFASL LEANKVHIDK SRFVDW MKW AYETRMYHAK KVALHPKVVE NYSKSLYKKK FSGVIKTNIE SVIKSYNGNK RVVAAELSFV IKYQGKDLEE MIKTYYE HL AVGRKALVDH INETGNAKLT KTQKGKIIGK EFTNDDKIIH KFIEIIDKKY KLAFFGTNPP IADRIAVISQ FINHLYNR A EGMVNITYED VKQEYLDRVN SSTDYYDIDR YLEFSSTRHE ARLRMTNAVI PAGHEMVILQ FLLVNRLKST SIDHEFIDK MPSDEFGEYL VDLVKRGNLA EAGQGKRLSA ADKIILLEVK TAKGTLSKIL SGEKLGKHAL RTIKQAWDFK NGRKNSLDEY PDFIQLIYH LQLLKRHNKS ISTVIEGSLG GGSFIVSHKD SHIPIGPKTS WKDIENLPED TQIFYKTTYW QNDKDTLRWS S SFHTIPST LDYSLCFTPR KEGRMFFHMD MAQAEVRIAF AVAKEMGLIN AILKGLDIHG FNANNAFDLG FAEDELYKIK QD PELDQLR SYAKMLTFAI LYGASVGSIA KQIKKPFDEA KKIYDGYFNA NPNFKKFVED NIAELSENFG FRYLPIFNHR FYI GNPYHY SIKQKGLNYI IQNLSSSLTA YTAYALYDDL RTNYGVEIQL LGFVHDAIEF EFDAKDLFII LDRMNYWYKE MPLE KWDIP SDFDFELGSS RYSGGSCKVK YNDDKSMADI KLEIKDYYND KEDILKLMKE SFNIIEDSLK KEDHPVEKHP FVFMI DGVK PDCRFREEVT DQYVYSAKIG LK

UniProtKB: DNA polymerase

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Macromolecule #2: DNA (25-MER)

MacromoleculeName: DNA (25-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 8.91375 KDa
SequenceString:
(DC)(DA)(DC)(DA)(DG)(DA)(DC)(DG)(DT)(DA) (DG)(DC)(DA)(DG)(DC)(DT)(DG)(DG)(DA)(DA) (DC)(DC)(DT)(DC)(DC)(DG)(DT)(DA)(DG)

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Macromolecule #3: DNA (29-MER)

MacromoleculeName: DNA (29-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 11.920648 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DC) (DC)(DT)(DA)(DC)(DG)(DG)(DA)(DG)(DG)(DT) (DT)(DC)(DC)(DA)(DG)(DC)(DT)(DG)(DC) (DT)(DA)(DC)(DG)(DT)(DC)(DT)(DG)(DT)(DG)

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Macromolecule #4: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: DG3
Molecular weightTheoretical: 491.182 Da
Chemical component information

ChemComp-DG3:
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.5
GridModel: Quantifoil Active R2/1 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 95 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30217
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

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