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- EMDB-63021: DNA polymerase holoenzyme -

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Basic information

Entry
Database: EMDB / ID: EMD-63021
TitleDNA polymerase holoenzyme
Map data
Sample
  • Virus: Monkeypox virus
    • 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)
  • Ligand: [[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
  • Ligand: MAGNESIUM ION
KeywordsDNA replication holoenzyme / DNA molecule / MPXV / F8-A22-E4 complex / VIRAL PROTEIN/DNA / VIRAL PROTEIN-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-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / 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: 2.73 Å
AuthorsWang N / Li Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Development of 2a as a Potent Inhibitor of MPXV: Mechanistic and Structural Characterization
Authors: Wang N / Li Y
History
DepositionJan 7, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63021.png

Downloads & links

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Map

FileDownload / File: emd_63021.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 480 pix.
= 254.4 Å		0.53 Å/pix.
x 480 pix.
= 254.4 Å		0.53 Å/pix.
x 480 pix.
= 254.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.53 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0031112786 - 5.8960323
Average (Standard dev.)0.0034706853 (±0.047081437)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63021_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63021_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63021_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Monkeypox virus

EntireName: Monkeypox virus
Components
  • Virus: Monkeypox virus
    • 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)
  • Ligand: [[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Monkeypox virus

SupramoleculeName: Monkeypox virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: DNA replication holoenzyme F8, A22 and E4 in complex with a DNA duplex and 2f-TP
NCBI-ID: 10244 / Sci species name: Monkeypox virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SUBSPECIES / Virus enveloped: No / Virus empty: No

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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: 117.057023 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: SMDVRCINWF ESHGENRFLY LKSRCRNGET VFIRFPHYFY YVVTDEIYQS LSPPPFNARP MGKMRTIDID ETISYNLDIK DRKCSVADM WLIEEPKKRS IQNATMDEFF NISWFYISNG ISPDGCYSLD EQYLTKINNG CYHCDDPRNC FAKEIPRFDI P RSYLFLDI ...String:
SMDVRCINWF ESHGENRFLY LKSRCRNGET VFIRFPHYFY YVVTDEIYQS LSPPPFNARP MGKMRTIDID ETISYNLDIK DRKCSVADM WLIEEPKKRS IQNATMDEFF NISWFYISNG ISPDGCYSLD EQYLTKINNG CYHCDDPRNC FAKEIPRFDI P RSYLFLDI ECHFDKKFPS VFINPISHTS YCYIDLSGKR LLFTLINEEM LTEQEIQEAV DRGCLRIQSL MEMDYERELV LC SEIVLLR IAKQLLELTF DYVVTFNGHN FDLRYITNRL ELLTGEKIIF RSPDKKEAVH LCIYERNQSS HKGVCGMANT TFH VNNNNG TIFFDLYSFI QKSEKLDSYK LDSISKNAFS CMGKVLNRGV REMTFIGDDT TDAKGKADTF AKVLTTGNYV TVDE DIICK VIRKDILENG FKVVLSCPTL PNDIYKLSFG KDDIDLAQMY KDYNLNIALD MARYCIHDAC LCQYLWEYYG VETKT DAGA ATYVLPQSMV FEYRASTIIK GPLLKLLLET KTILVRSETK QKFPYEGGKV FAPKQKMFSN NVLIFDYNSL YPNVCI FGN LSPETLVGVV VSTNRLEEEI NNQLLLQKYP PPRYITVHCE PRLPNLISEI AIFDRSIEGT IPRLLRTFLA ERARYKK ML KQATSSTEKA IYDSMQYTYK IVANSVYGLM GFRNSALYSY ASAKSCTSIG RRMILYLESV LNGAELSNGM LRFANTLS N PFYMDDRDIN PIVKTSLPID YRFRFRSVYG DTDSVFTEID SQDVDKSIEI AKELERLINS RVLFNNFKIE FEAVYKNLI MQSKKKYTTM KYSASSNSKS VPERINKGTS ETRRDVSKFH KNMIKTYKTR LSEMLSEGRM NSNQVCIDIL RSLETDLRSE FDSRSSPLE LFMLSRMHHS NYKSADNPNM YLVTEYNKNN PETIELGERY YFAYICPANV PWTKKLVNIK TYETIIDRSF K LGSNQRIF YEVYFKRLTS EIVNLLDNKV LCISFFQRMF GSRPTFW

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: 7.681985 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)(DC)

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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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Macromolecule #6: [[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-[5-methyl-2,4-bis(oxida...

MacromoleculeName: [[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1EKM
Molecular weightTheoretical: 500.159 Da

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 347619
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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