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- EMDB-34731: The structure of MPXV polymerase holoenzyme in replicating state -
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Open data
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Basic information
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Title | The structure of MPXV polymerase holoenzyme in replicating state | |||||||||
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![]() | MPXV / Polymerase / Replication / REPLICATION-DNA complex | |||||||||
Function / homology | ![]() viral DNA genome replication / uracil DNA N-glycosylase activity / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / base-excision repair, gap-filling / DNA replication / DNA recombination / DNA-directed DNA polymerase ...viral DNA genome replication / uracil DNA N-glycosylase activity / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / base-excision repair, gap-filling / DNA replication / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleotide binding / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Peng Q / Xie YF / Kuai L / Wang H / Qi JX / Gao F / Shi Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of monkeypox virus DNA polymerase holoenzyme. Authors: Qi Peng / Yufeng Xie / Lu Kuai / Han Wang / Jianxun Qi / George F Gao / Yi Shi / ![]() Abstract: The World Health Organization declared mpox (or monkeypox) a public health emergency of international concern in July 2022, and prophylactic and therapeutic measures are in urgent need. The monkeypox ...The World Health Organization declared mpox (or monkeypox) a public health emergency of international concern in July 2022, and prophylactic and therapeutic measures are in urgent need. The monkeypox virus (MPXV) has its own DNA polymerase F8, together with the processive cofactors A22 and E4, constituting the polymerase holoenzyme for genome replication. Here, we determined the holoenzyme structure in complex with DNA using cryo-electron microscopy at the global resolution of ~2.8 angstroms. The holoenzyme possesses an architecture that suggests a "forward sliding clamp" processivity mechanism for viral DNA replication. MPXV polymerase has a DNA binding mode similar to that of other B-family DNA polymerases from different species. These findings reveal the mechanism of the MPXV genome replication and may guide the development of anti-poxvirus drugs. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 111 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19 KB 19 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 35.7 KB | ||
Filedesc metadata | ![]() | 7 KB | ||
Others | ![]() ![]() | 116 MB 116 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 742.7 KB | Display | ![]() |
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Full document | ![]() | 742.3 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hg1MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34731_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34731_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : MPXV DNA polymerase holoenzyme
Entire | Name: MPXV DNA polymerase holoenzyme |
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Components |
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-Supramolecule #1: MPXV DNA polymerase holoenzyme
Supramolecule | Name: MPXV DNA polymerase holoenzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: DNA polymerase
Macromolecule | Name: DNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 119.939062 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 FLDIECHFDK 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 |
-Macromolecule #2: E4R
Macromolecule | Name: E4R / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: uracil-DNA glycosylase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.107742 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #3: DNA polymerase processivity factor component A20
Macromolecule | Name: DNA polymerase processivity factor component A20 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 49.203926 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #4: DNA (25-MER)
Macromolecule | Name: DNA (25-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.681985 KDa |
Sequence | String: (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) |
-Macromolecule #5: DNA (38-MER)
Macromolecule | Name: DNA (38-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.677539 KDa |
Sequence | String: (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) |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: THYMIDINE-5'-TRIPHOSPHATE
Macromolecule | Name: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: TTP |
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Molecular weight | Theoretical: 482.168 Da |
Chemical component information | ![]() ChemComp-TTP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 |