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Yorodumi- EMDB-34929: Monkeypox virus DNA replication holoenzyme F8, A22 and E4 complex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34929 | |||||||||
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Title | Monkeypox virus DNA replication holoenzyme F8, A22 and E4 complex in a DNA binding form | |||||||||
Map data | Please use this map | |||||||||
Sample |
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Keywords | Monkeypox virus / DNA replication holoenzyme / DNA replication machinery / F8 / A22 / E4 / DNA polymerase / B-family DNA polymerase / uracil-DNA glycosylase / MPXV / orthopoxvirus / poxviridae / F8-A22-E4 complex / DNA processivity factor / 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 | |||||||||
Biological species | Monkeypox virus / DNA molecule (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.01 Å | |||||||||
Authors | Xu Y / Wu Y / Zhang Y / Fan R / Yang Y / Li D / Yang B / Zhang Z / Dong C / Zhang X ...Xu Y / Wu Y / Zhang Y / Fan R / Yang Y / Li D / Yang B / Zhang Z / Dong C / Zhang X / Tang X / Dong H | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Structure of DNA replication machinery from human monkeypox virus Authors: Xu YX / Wu YQ / Zhang YY / Fan RX / Yang YX / Li DY / Yang B / Zhang ZY / Dong CJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34929.map.gz | 230.2 MB | EMDB map data format | |
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Header (meta data) | emd-34929-v30.xml emd-34929.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
Images | emd_34929.png | 41.5 KB | ||
Filedesc metadata | emd-34929.cif.gz | 7.2 KB | ||
Others | emd_34929_half_map_1.map.gz emd_34929_half_map_2.map.gz | 226.7 MB 226.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34929 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34929 | HTTPS FTP |
-Related structure data
Related structure data | 8hpaMC 8hoyC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34929.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Please use this map | ||||||||||||||||||||
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: Please use this map
File | emd_34929_half_map_1.map | ||||||||||||
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Annotation | Please use this map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: please use this map
File | emd_34929_half_map_2.map | ||||||||||||
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Annotation | please use this map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Monkeypox virus replication holoenzyme F8-A22-E4 complex with DNA
Entire | Name: Monkeypox virus replication holoenzyme F8-A22-E4 complex with DNA |
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Components |
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-Supramolecule #1: Monkeypox virus replication holoenzyme F8-A22-E4 complex with DNA
Supramolecule | Name: Monkeypox virus replication holoenzyme F8-A22-E4 complex with DNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: F8-A22-E4 complex with DNA |
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Source (natural) | Organism: Monkeypox virus |
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: Monkeypox virus |
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: DNA polymerase processivity factor component A20
Macromolecule | Name: DNA polymerase processivity factor component A20 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Monkeypox virus |
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 #3: E4R
Macromolecule | Name: E4R / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: uracil-DNA glycosylase |
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Source (natural) | Organism: Monkeypox virus |
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 #4: DNA (5'-D(P*AP*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*CP*G)-3')
Macromolecule | Name: DNA (5'-D(P*AP*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*CP*G)-3') type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: DNA molecule (others) |
Molecular weight | Theoretical: 8.14825 KDa |
Sequence | String: (DA)(DT)(DG)(DG)(DT)(DA)(DG)(DG)(DG)(DG) (DA)(DA)(DG)(DG)(DA)(DT)(DC)(DG)(DT)(DA) (DT)(DG)(DG)(DC)(DC)(DT) |
-Macromolecule #5: DNA (5'-D(*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
Macromolecule | Name: DNA (5'-D(*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3') type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: DNA molecule (others) |
Molecular weight | Theoretical: 6.921475 KDa |
Sequence | String: (DA)(DG)(DG)(DC)(DC)(DA)(DT)(DA)(DC)(DG) (DA)(DT)(DC)(DC)(DT)(DT)(DC)(DC)(DC)(DC) (DT)(DA)(DC) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Details: 25mM HEPES pH 8.0, 300mM NaCl, 5% (w/v) glycerol, and 1 mM TCEP |
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Vitrification | Cryogen name: ETHANE |
Details | This is a complex of F8-A22-E4 and DNA |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
Image recording | Film 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 |
-Image processing
Particle selection | Details: 1063499 |
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Startup model | Type of model: OTHER / Details: Alphfold2 prediction |
Initial angle assignment | Type: NOT APPLICABLE |
Final 3D classification | Number classes: 6 / Software - Name: cryoSPARC |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 72237 |
Details | The selected movies are corrected with motion correct |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8hpa: |