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- EMDB-36069: Monkeypox virus DNA replication holoenzyme F8, A22 and E4 in comp... -
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Open data
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Basic information
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Title | Monkeypox virus DNA replication holoenzyme F8, A22 and E4 in complex with a DNA duplex and cidofovir diphosphate | |||||||||
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![]() | Monkeypox virus / DNA replication holoenzyme / DNA replication machinery / DNA polymerase / B-family DNA polymerase / uracil-DNA glycosylase / MPXV / orthopoxvirus / poxviridae / DNA processivity factor / DNA / CDVpp / cidofovir diphosphate / VIRAL PROTEIN | |||||||||
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 recombination / DNA replication / 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 recombination / DNA replication / 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: 2.79 Å | |||||||||
![]() | Xu Y / Wu Y / Wu X / Zhang Y / Yang Y / Li D / Yang B / Gao K / Zhang Z / Dong C ...Xu Y / Wu Y / Wu X / Zhang Y / Yang Y / Li D / Yang B / Gao K / Zhang Z / Dong C / Tang X / Dong H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of human mpox viral DNA replication inhibition by brincidofovir and cidofovir. Authors: Yunxia Xu / Yaqi Wu / Xiaoying Wu / Yuanyuan Zhang / Yaxue Yang / Danyang Li / Biao Yang / Kaiting Gao / Zhengyu Zhang / Changjiang Dong / ![]() Abstract: Mpox virus has wildly spread over 108 non-endemic regions in the world since May 2022. DNA replication of mpox is performed by DNA polymerase machinery F8-A22-E4, which is known as a great drug ...Mpox virus has wildly spread over 108 non-endemic regions in the world since May 2022. DNA replication of mpox is performed by DNA polymerase machinery F8-A22-E4, which is known as a great drug target. Brincidofovir and cidofovir are reported to have broad-spectrum antiviral activity against poxviruses, including mpox virus in animal models. However, the molecular mechanism is not understood. Here we report cryogenic electron microscopy structures of mpox viral F8-A22-E4 in complex with a DNA duplex, or dCTP and the DNA duplex, or cidofovir diphosphate and the DNA duplex at resolution of 3.22, 2.98 and 2.79 Å, respectively. Our structural work and DNA replication inhibition assays reveal that cidofovir diphosphate is located at the dCTP binding position with a different conformation to compete with dCTP to incorporate into the DNA and inhibit DNA synthesis. Conformation of both F8-A22-E4 and DNA is changed from the pre-dNTP binding state to DNA synthesizing state after dCTP or cidofovir diphosphate is bound, suggesting a coupling mechanism. This work provides the structural basis of DNA synthesis inhibition by brincidofovir and cidofovir, providing a rational strategy for new therapeutical development for mpox virus and other pox viruses. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 230.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22 KB 22 KB | Display Display | ![]() |
Images | ![]() | 68.3 KB | ||
Filedesc metadata | ![]() | 7.3 KB | ||
Others | ![]() ![]() | 226.7 MB 226.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8j8gMC ![]() 8j86C ![]() 8j8fC 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
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36069_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36069_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Monkeypox virus replication holoenzyme F8-A22-E4 in complex with ...
Entire | Name: Monkeypox virus replication holoenzyme F8-A22-E4 in complex with DNA duplex and cidofovir diphosphate |
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Components |
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-Supramolecule #1: Monkeypox virus replication holoenzyme F8-A22-E4 in complex with ...
Supramolecule | Name: Monkeypox virus replication holoenzyme F8-A22-E4 in complex with DNA duplex and cidofovir diphosphate type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 Details: F8-A22-E4 in complex with DNA duplex and cidofovir diphosphate |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 191 kDa/nm |
-Macromolecule #1: DNA polymerase
Macromolecule | Name: DNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 120.041156 KDa |
Recombinant expression | Organism: Insect expression vector pBlueBachsGCA1 (others) |
Sequence | String: MHHHHHHHHD YDIPTTENLY FQGMDVRCIN WFESHGENRF LYLKSRCRNG ETVFIRFPHY FYYVVTDEIY QSLSPPPFNA RPMGKMRTI DIDETISYNL DIKDRKCSVA DMWLIEEPKK RSIQNATMDE FFNISWFYIS NGISPDGCYS LDEQYLTKIN N GCYHCDDP ...String: MHHHHHHHHD YDIPTTENLY FQGMDVRCIN WFESHGENRF LYLKSRCRNG ETVFIRFPHY FYYVVTDEIY QSLSPPPFNA RPMGKMRTI DIDETISYNL DIKDRKCSVA DMWLIEEPKK RSIQNATMDE FFNISWFYIS NGISPDGCYS LDEQYLTKIN N GCYHCDDP RNCFAKEIPR FDIPRSYLFL DIECHFDKKF PSVFINPISH TSYCYIDLSG KRLLFTLINE EMLTEQEIQE AV DRGCLRI QSLMEMDYER ELVLCSEIVL LRIAKQLLEL TFDYVVTFNG HNFDLRYITN RLELLTGEKI IFRSPDKKEA VHL CIYERN QSSHKGVCGM ANTTFHVNNN NGTIFFDLYS FIQKSEKLDS YKLDSISKNA FSCMGKVLNR GVREMTFIGD DTTD AKGKA DTFAKVLTTG NYVTVDEDII CKVIRKDILE NGFKVVLSCP TLPNDIYKLS FGKDDIDLAQ MYKDYNLNIA LDMAR YCIH DACLCQYLWE YYGVETKTDA GAATYVLPQS MVFEYRASTI IKGPLLKLLL ETKTILVRSE TKQKFPYEGG KVFAPK QKM FSNNVLIFDY NSLYPNVCIF GNLSPETLVG VVVSTNRLEE EINNQLLLQK YPPPRYITVH CEPRLPNLIS EIAIFDR SI EGTIPRLLRT FLAERARYKK MLKQATSSTE KAIYDSMQYT YKIVANSVYG LMGFRNSALY SYASAKSCTS IGRRMILY L ESVLNGAELS NGMLRFANTL SNPFYMDDRD INPIVKTSLP IDYRFRFRSV YGDTDSVFTE IDSQDVDKSI EIAKELERL INSRVLFNNF KIEFEAVYKN LIMQSKKKYT TMKYSASSNS KSVPERINKG TSETRRDVSK FHKNMIKTYK TRLSEMLSEG RMNSNQVCI DILRSLETDL RSEFDSRSSP LELFMLSRMH HSNYKSADNP NMYLVTEYNK NNPETIELGE RYYFAYICPA N VPWTKKLV NIKTYETIID RSFKLGSNQR IFYEVYFKRL TSEIVNLLDN KVLCISFFQR MFGSRPTFYE A 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: 27.883709 KDa |
Recombinant expression | Organism: Insect expression vector pBlueBachsGCA1 (others) |
Sequence | String: MHHHHHHDYD IPTTENLYFQ GASMNSVTIS HAPYTITYHD DWEPVMSQLV EFYNEVASWL LRDETSPIPD KFFIQLKQPL RNKRVCVCG IDPYPKDGTG VPFESPNFTK KSIKEIASSI SRLTGVIDYK GYNLNIIDGV IPWNYYLSCK LGETKSHAIY W DKISKLLL ...String: MHHHHHHDYD IPTTENLYFQ GASMNSVTIS HAPYTITYHD DWEPVMSQLV EFYNEVASWL LRDETSPIPD KFFIQLKQPL RNKRVCVCG IDPYPKDGTG VPFESPNFTK KSIKEIASSI SRLTGVIDYK GYNLNIIDGV IPWNYYLSCK LGETKSHAIY W DKISKLLL QHITKHVSVL YCLGKTDFSN IRAKLESPVT TIVGYHPAAR DHQFEKDRSF EIINVLLELD NKTPINWAQG FI Y 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: Insect expression vector pBlueBachsGCA1 (others) |
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 (5'-D(P*AP*GP*CP*TP*GP*CP*TP*AP*TP*GP*AP*GP*AP*TP*TP*AP*AP*GP...
Macromolecule | Name: DNA (5'-D(P*AP*GP*CP*TP*GP*CP*TP*AP*TP*GP*AP*GP*AP*TP*TP*AP*AP*GP*TP*TP*AP*T)-3') type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: DNA molecule (others) |
Molecular weight | Theoretical: 7.438825 KDa |
Sequence | String: (DA)(DG)(DC)(DT)(DG)(DC)(DT)(DA)(DT)(DG) (DT)(DG)(DA)(DG)(DA)(DT)(DT)(DA)(DA)(DG) (DT)(DT)(DA)(DT) |
-Macromolecule #5: DNA (5'-D(P*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP...
Macromolecule | Name: DNA (5'-D(P*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP*CP*TP*TP*AP*AP*TP*CP*TP*CP*AP*CP*AP*TP*AP*GP*CP*AP*GP*CP*T)-3') type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: DNA molecule (others) |
Molecular weight | Theoretical: 11.60548 KDa |
Sequence | String: (DG)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DG)(DA)(DT)(DA)(DA)(DC)(DT) (DT)(DA)(DA)(DT)(DC)(DT)(DC)(DA)(DC) (DA)(DT)(DA)(DG)(DC)(DA)(DG)(DC)(DT) |
-Macromolecule #6: [(2S)-1-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-prop...
Macromolecule | Name: [(2S)-1-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-propan-2-yl]oxymethyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphinic acid type: ligand / ID: 6 / Number of copies: 1 / Formula: TXJ |
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Molecular weight | Theoretical: 439.147 Da |
-Macromolecule #7: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-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 Details: 25 mM MOPS, pH 7.0, 200 mM NaCl, 5% (w/v) glycerol, 1 mM TCEP |
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Vitrification | Cryogen name: ETHANE |
Details | F8-A22-E4 in complex with a DNA duplex and cidofovir diphosphate |
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Electron microscopy
Microscope | TFS 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: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-8j8g: |