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- EMDB-62200: MPXV DNA polymerase complex in editing state 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-62200
TitleMPXV DNA polymerase complex in editing state 2
Map data
Sample
  • Complex: MPXV DNA polymerase in complex with primer/4U template DNA
    • Protein or peptide: DNA polymerase
    • Protein or peptide: Uracil-DNA glycosylase
    • Protein or peptide: DNA polymerase processivity factor
    • DNA: DNA (25-MER)
    • DNA: DNA (38-MER)
Keywordscomplex / replicate / DNA / mpox / polymerase / REPLICATION/DNA / REPLICATION-DNA complex
Function / homology
Function and homology information


uracil DNA N-glycosylase activity / viral DNA genome replication / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / hydrolase activity / DNA repair / nucleotide binding / DNA binding
Similarity search - Function
DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / Chordopoxvirus A20R / Chordopoxvirus A20R protein / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like domain superfamily / : ...DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / Chordopoxvirus A20R / Chordopoxvirus A20R protein / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like domain superfamily / : / 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 / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase / DNA polymerase processivity factor / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMonkeypox virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsXie YF / Kuai L / Peng Q / Wang Q / Wang H / Li XM / Qi JX / Ding Q / Shi Y / Gao F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: MPXV DNA polymerase complex in editing state 2
Authors: Xie YF / Kuai L / Peng Q / Wang Q / Wang H / Li XM / Qi JX / Ding Q / Shi Y / Gao F
History
DepositionOct 27, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62200.png

Downloads & links

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Map

FileDownload / File: emd_62200.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0018079153 - 2.2853346
Average (Standard dev.)0.0014282702 (±0.026153238)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62200_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_62200_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 : MPXV DNA polymerase in complex with primer/4U template DNA

EntireName: MPXV DNA polymerase in complex with primer/4U template DNA
Components
  • Complex: MPXV DNA polymerase in complex with primer/4U template DNA
    • Protein or peptide: DNA polymerase
    • Protein or peptide: Uracil-DNA glycosylase
    • Protein or peptide: DNA polymerase processivity factor
    • DNA: DNA (25-MER)
    • DNA: DNA (38-MER)

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Supramolecule #1: MPXV DNA polymerase in complex with primer/4U template DNA

SupramoleculeName: MPXV DNA polymerase in complex with primer/4U template DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Monkeypox 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: Monkeypox virus
Molecular weightTheoretical: 119.837016 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MWSHPQFEKG SGSWSHPQFE KGSGSMDVRC INWFESHGEN RFLYLKSRCR NGETVFIRFP HYFYYVVTDE IYQSLSPPPF NARPMGKMR TIDIDETISY NLDIKDRKCS VADMWLIEEP KKRSIQNATM DEFFNISWFY ISNGISPDGC YSLDEQYLTK I NNGCYHCD ...String:
MWSHPQFEKG SGSWSHPQFE KGSGSMDVRC INWFESHGEN RFLYLKSRCR NGETVFIRFP HYFYYVVTDE IYQSLSPPPF NARPMGKMR TIDIDETISY NLDIKDRKCS VADMWLIEEP KKRSIQNATM DEFFNISWFY ISNGISPDGC YSLDEQYLTK I NNGCYHCD DPRNCFAKEI PRFDIPRSYL FLAIACHFDK KFPSVFINPI SHTSYCYIDL SGKRLLFTLI NEEMLTEQEI QE AVDRGCL RIQSLMEMDY ERELVLCSEI VLLRIAKQLL ELTFDYVVTF NGHNFDLRYI TNRLELLTGE KIIFRSPDKK EAV HLCIYE RNQSSHKGVC GMANTTFHVN NNNGTIFFDL YSFIQKSEKL DSYKLDSISK NAFSCMGKVL NRGVREMTFI GDDT TDAKG KADTFAKVLT TGNYVTVDED IICKVIRKDI LENGFKVVLS CPTLPNDIYK LSFGKDDIDL AQMYKDYNLN IALDM ARYC IHDACLCQYL WEYYGVETKT DAGAATYVLP QSMVFEYRAS TIIKGPLLKL LLETKTILVR SETKQKFPYE GGKVFA PKQ KMFSNNVLIF DYNSLYPNVC IFGNLSPETL VGVVVSTNRL EEEINNQLLL QKYPPPRYIT VHCEPRLPNL ISEIAIF DR SIEGTIPRLL RTFLAERARY KKMLKQATSS TEKAIYDSMQ YTYKIVANSV YGLMGFRNSA LYSYASAKSC TSIGRRMI L YLESVLNGAE LSNGMLRFAN TLSNPFYMDD RDINPIVKTS LPIDYRFRFR SVYGDTDSVF TEIDSQDVDK SIEIAKELE RLINSRVLFN NFKIEFEAVY KNLIMQSKKK YTTMKYSASS NSKSVPERIN KGTSETRRDV SKFHKNMIKT YKTRLSEMLS EGRMNSNQV CIDILRSLET DLRSEFDSRS SPLELFMLSR MHHSNYKSAD NPNMYLVTEY NKNNPETIEL GERYYFAYIC P ANVPWTKK LVNIKTYETI IDRSFKLGSN QRIFYEVYFK RLTSEIVNLL DNKVLCISFF QRMFGSRPTF YEA

UniProtKB: DNA polymerase

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Macromolecule #2: Uracil-DNA glycosylase

MacromoleculeName: Uracil-DNA glycosylase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 25.107742 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MNSVTISHAP YTITYHDDWE PVMSQLVEFY NEVASWLLRD ETSPIPDKFF IQLKQPLRNK RVCVCGIDPY PKDGTGVPFE SPNFTKKSI KEIASSISRL TGVIDYKGYN LNIIDGVIPW NYYLSCKLGE TKSHAIYWDK ISKLLLQHIT KHVSVLYCLG K TDFSNIRA ...String:
MNSVTISHAP YTITYHDDWE PVMSQLVEFY NEVASWLLRD ETSPIPDKFF IQLKQPLRNK RVCVCGIDPY PKDGTGVPFE SPNFTKKSI KEIASSISRL TGVIDYKGYN LNIIDGVIPW NYYLSCKLGE TKSHAIYWDK ISKLLLQHIT KHVSVLYCLG K TDFSNIRA KLESPVTTIV GYHPAARDHQ FEKDRSFEII NVLLELDNKT PINWAQGFIY

UniProtKB: Uracil-DNA glycosylase

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Macromolecule #3: DNA polymerase processivity factor

MacromoleculeName: DNA polymerase processivity factor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 49.203926 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MTSSADLTNL KELLSLYKSL RFSDSVAIEK YNSLVEWGTS TYWKIGVQKV TNVETSISDY YDEVKNKPFN IDPGYYIFLP VYFGSVFIY SKGKNMVELG SGNSFQIPDE IRSACNKVLD SDNGIDFLRF VLLNNRWIME DAISKYQSPV NIFKLASEYG L NIPNYLEI ...String:
MTSSADLTNL KELLSLYKSL RFSDSVAIEK YNSLVEWGTS TYWKIGVQKV TNVETSISDY YDEVKNKPFN IDPGYYIFLP VYFGSVFIY SKGKNMVELG SGNSFQIPDE IRSACNKVLD SDNGIDFLRF VLLNNRWIME DAISKYQSPV NIFKLASEYG L NIPNYLEI EIEEDTLFDD ELYSIMERSF DDTFPKISIS YIKLGELKRQ VVDFFKFSFM YIESIKVDRI GDNIFIPSVI TK SGKKILV KDVDHLIRSK VREHTFVKVK KKNTFSILYD YDGNGTETRG EVIKRIIDTI GRDYYVNGKY FSKVGIAGLK QLT NKLDIN ECATVDELVD EINKSGTVKR KIKNQSVFDL SRECLGYPEA DFITLVNNMR FKIENCKVVN FNIENTNCLN NPSI ETIYG NFNQFVSIFN TVTDVKKRLF E

UniProtKB: DNA polymerase processivity factor

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Macromolecule #4: DNA (25-MER)

MacromoleculeName: DNA (25-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 7.696997 KDa
SequenceString:
(DA)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DC)(DC) (DA)(DT)(DG)(DA)(DT)(DT)(DA)(DC)(DG)(DA) (DA)(DT)(DT)(DG)(DT)

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Macromolecule #5: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 11.677539 KDa
SequenceString:
(DC)(DT)(DG)(DC)(DA)(DC)(DG)(DA)(DA)(DT) (DT)(DA)(DA)(DG)(DC)(DA)(DA)(DT)(DT)(DC) (DG)(DT)(DA)(DA)(DT)(DC)(DA)(DT)(DG) (DG)(DT)(DC)(DA)(DT)(DA)(DG)(DC)(DT)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8hg1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127422
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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