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- EMDB-53228: YerA41 family-A DNA polymerase -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53228
TitleYerA41 family-A DNA polymerase
Map data
Sample
  • Complex: YerA41 family-A DNA polymerase
    • Protein or peptide: DNA polymerase
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 speciesThermus phage phiLo (virus) / Yersinia phage YerA41 (virus)
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
Authors: Missoury S / Delarue M
History
DepositionMar 21, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53228.png

Downloads & links

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Map

FileDownload / File: emd_53228.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: 0.172
Minimum - Maximum-1.1452062 - 1.7069436
Average (Standard dev.)-0.000782288 (±0.026747093)
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_53228_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_53228_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 : YerA41 family-A DNA polymerase

EntireName: YerA41 family-A DNA polymerase
Components
  • Complex: YerA41 family-A DNA polymerase
    • Protein or peptide: DNA polymerase

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Supramolecule #1: YerA41 family-A DNA polymerase

SupramoleculeName: YerA41 family-A DNA polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus phage phiLo (virus)

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Macromolecule #1: DNA polymerase

MacromoleculeName: DNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Yersinia phage YerA41 (virus)
Molecular weightTheoretical: 152.888891 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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 LVRTGKNNLV PPMVQIDPKF HHISELESIY HSKWQPDEHK GFDFETRNFP 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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: 2.0 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: 50000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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