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- EMDB-36069: Monkeypox virus DNA replication holoenzyme F8, A22 and E4 in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-36069
TitleMonkeypox virus DNA replication holoenzyme F8, A22 and E4 in complex with a DNA duplex and cidofovir diphosphate
Map data
Sample
  • Complex: Monkeypox virus replication holoenzyme F8-A22-E4 in complex with DNA duplex and cidofovir diphosphate
    • Protein or peptide: DNA polymerase
    • Protein or peptide: E4R
    • Protein or peptide: DNA polymerase processivity factor component A20
    • DNA: 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')
    • DNA: 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')
  • Ligand: [(2S)-1-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-propan-2-yl]oxymethyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphinic acid
  • Ligand: CALCIUM IONCalcium
KeywordsMonkeypox 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
Function and homology information


viral DNA genome replication / uracil DNA N-glycosylase activity / DNA recombination / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA repair / 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 polymerase family B signature. ...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, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional 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 processivity factor / Uracil-DNA glycosylase / DNA polymerase
Similarity search - Component
Biological speciesMonkeypox virus / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsXu 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 China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32250710142 China
CitationJournal: To Be Published
Title: Structural basis of human monkeypox viral DNA replication inhibition by brincidofovir and cidofovir
Authors: Xu YX / Wu YQ / Wu XY / Zhang YY / Yang YX / Li DY / Yang B / Gao K / Zhang ZY / Dong CJ
History
DepositionMay 1, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36069.png

Downloads & links

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Map

FileDownload / File: emd_36069.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-1.4863821 - 1.9545795
Average (Standard dev.)0.0000377368 (±0.028826239)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36069_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_36069_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 : Monkeypox virus replication holoenzyme F8-A22-E4 in complex with ...

EntireName: Monkeypox virus replication holoenzyme F8-A22-E4 in complex with DNA duplex and cidofovir diphosphate
Components
  • Complex: Monkeypox virus replication holoenzyme F8-A22-E4 in complex with DNA duplex and cidofovir diphosphate
    • Protein or peptide: DNA polymerase
    • Protein or peptide: E4R
    • Protein or peptide: DNA polymerase processivity factor component A20
    • DNA: 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')
    • DNA: 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')
  • Ligand: [(2S)-1-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-propan-2-yl]oxymethyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphinic acid
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: Monkeypox virus replication holoenzyme F8-A22-E4 in complex with ...

SupramoleculeName: 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
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 191 kDa/nm

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Macromolecule #1: DNA polymerase

MacromoleculeName: DNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 120.041156 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBachsGCA1 (others)
SequenceString: 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

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Macromolecule #2: E4R

MacromoleculeName: E4R / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: uracil-DNA glycosylase
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 27.883709 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBachsGCA1 (others)
SequenceString: 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

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Macromolecule #3: DNA polymerase processivity factor component A20

MacromoleculeName: DNA polymerase processivity factor component A20 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 49.203926 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBachsGCA1 (others)
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 (5'-D(P*AP*GP*CP*TP*GP*CP*TP*AP*TP*GP*AP*GP*AP*TP*TP*AP*AP*GP...

MacromoleculeName: 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
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 7.438825 KDa
SequenceString:
(DA)(DG)(DC)(DT)(DG)(DC)(DT)(DA)(DT)(DG) (DT)(DG)(DA)(DG)(DA)(DT)(DT)(DA)(DA)(DG) (DT)(DT)(DA)(DT)

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Macromolecule #5: DNA (5'-D(P*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP...

MacromoleculeName: 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
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 11.60548 KDa
SequenceString:
(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)

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Macromolecule #6: [(2S)-1-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-prop...

MacromoleculeName: [(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
Molecular weightTheoretical: 439.147 Da

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 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: 7
Details: 25 mM MOPS, pH 7.0, 200 mM NaCl, 5% (w/v) glycerol, 1 mM TCEP
VitrificationCryogen name: ETHANE
DetailsF8-A22-E4 in complex with a DNA duplex and cidofovir diphosphate

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionDetails: 17,907,684
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8j86


Details: F8-A22_E4 in complex a DNA complex
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 6 / Resolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1151891
DetailsThe selected movies are corrected with motion correct

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8j8g:
Monkeypox virus DNA replication holoenzyme F8, A22 and E4 in complex with a DNA duplex and cidofovir diphosphate

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