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- EMDB-52894: DNAP phiLo bound to modified DNA-closed conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-52894
TitleDNAP phiLo bound to modified DNA-closed conformation
Map data
Sample
  • Complex: DNAP phiLo
    • Protein or peptide: phiLo
KeywordsDNA polymerase / glyscosylase / DNA BINDING PROTEIN
Biological speciesThermus phage phiLo (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMissoury S / Delarue M
Funding support France, 1 items
OrganizationGrant numberCountry
Not funded France
CitationJournal: To Be Published
Title: DNAP phiLo bound to modified DNA-closed conformation
Authors: Missoury S / Delarue M
History
DepositionFeb 24, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52894.png

Downloads & links

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Map

FileDownload / File: emd_52894.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 560 pix.
= 319.2 Å		0.57 Å/pix.
x 560 pix.
= 319.2 Å		0.57 Å/pix.
x 560 pix.
= 319.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.122334845 - 0.18977368
Average (Standard dev.)-0.00005162013 (±0.003042165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 319.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52894_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_52894_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 : DNAP phiLo

EntireName: DNAP phiLo
Components
  • Complex: DNAP phiLo
    • Protein or peptide: phiLo

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Supramolecule #1: DNAP phiLo

SupramoleculeName: DNAP phiLo / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus phage phiLo (virus)
Molecular weightTheoretical: 158 KDa

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Macromolecule #1: phiLo

MacromoleculeName: phiLo / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus phage phiLo (virus)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSTVLIGYVN IRPGKGGKLI NQDVWKYFEK YVPAHFEDVD LLLFNPQTLP NLSDMIEDLN KYDNIIVTGR EPLKYLGLED AEIDRHSQFS NDDLADDQEE EEEVEDTDNE EDDDSEDDES GEESDGDDDD DDEFKVKKTK KSDNKIEVMR YFGLINNNPA LKFNKIHVMY ...String:
MSTVLIGYVN IRPGKGGKLI NQDVWKYFEK YVPAHFEDVD LLLFNPQTLP NLSDMIEDLN KYDNIIVTGR EPLKYLGLED AEIDRHSQFS NDDLADDQEE EEEVEDTDNE EDDDSEDDES GEESDGDDDD DDEFKVKKTK KSDNKIEVMR YFGLINNNPA LKFNKIHVMY SLMMYIAKDK INVFHFDLLN RTGKNNLVPP MVQIDPKFHH ISELESIYHS KWQPDEHKGF TRNFPFEPRF RLLGFSLAND TYQAYFYFSR DDDKYAQEME QYRSVMVKIF LEDAKKLHTY NNKFENNAVL DQLRERIFFE DSRIYTQMLK TRGSLKFSAN LFLGVPVWNE GINTFMKNYK EFVAWMKDYR ELSMIEESVI DKNAYEITSI KDLLSSDDKS TLIKLLGLTE TDKVKDRSRL EFKLTDDGDK KEPTYKLTTY VVETYFDLLL DPIKFVEKAM EHSQKYEQSF FKFFMTYQDR LEGKFKLTNL LTYFIKNYNE WQSCGIGDMG YYCILDGYYT VKLKEMLYDT NYDGCADGYI YYLYQSHFAS LLEANKVHID KSRFVDWMKW AYETRMYHAK KVALHPKVVE NYSKSLYKKK FSGVIKTNIE SVIKSYNGNK RVVAAELSFV IKYQGKDLEE MIKTYYEHLA VGRKALVDHI NETGNAKLTK TQKGKIIGKE FTNDDKIIHK FIEIIDKKYK LAFFGTNPPI ADRIAVISQF INHLYNRAEG MVNITYEDVK QEYLDRVNSS TDYYDIDRYL EFSSTRHEAR LRMTNAVIPA GHEMVILQFL LVNRLKSTSI DHEFIDKMPS DEFGEYLVDL VKRGNLAEAG QGKRLSAADK IILLEVKTAK GTLSKILSGE KLGKHALRTI KQAWDFKNGR KNSLDEYPDF IQLIYHLQLL KRHNKSISTV IEGSLGGGSF IVSHKDSHIP IGPKTSWKDI ENLPEDTQIF YKTTYWQNDK DTLRWSSSFH TIPSTLDYSL CFTPRKEGRM FFHMDMAQAE VRIAFAVAKE MGLINAILKG LDIHGFNANN AFDLGFAEDE LYKIKQDPEL DQLRSYAKML TFAILYGASV GSIAKQIKKP FDEAKKIYDG YFNANPNFKK FVEDNIAELS ENFGFRYLPI FNHRFYIGNP YHYSIKQKGL NYIIQNLSSS LTAYTAYALY DDLRTNYGVE IQLLGFVHDA IEFEFDAKDL FIILDRMNYW YKEMPLEKWD IPSDFDFELG SSRYSGGSCK VKYNDDKSMA DIKLEIKDYY NDKEDILKLM KESFNIIEDS LKKEDHPVEK HPFVFMIDGV KPDCRFREEV TDQYVYSAKI GLK

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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

Concentration2 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Number images used: 70000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1
FSC plot (resolution estimation)

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