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Yorodumi- EMDB-37722: Structure of monkeypox virus polymerase complex F8-A22-E4-H5 with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37722 | |||||||||
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Title | Structure of monkeypox virus polymerase complex F8-A22-E4-H5 with endogenous DNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Viral DNA replication / monkeypox virus / polymerase / H5 / VIRAL PROTEIN | |||||||||
Biological species | Monkeypox virus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Wang X / Li N / Gao N | |||||||||
Funding support | China, 1 items
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Citation | Journal: Mol Cell / Year: 2023 Title: Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5. Authors: Xiaohan Wang / Liangwen Ma / Ningning Li / Ning Gao / Abstract: The DNA replication of mpox virus is performed by the viral polymerase F8 and also requires other viral factors, including processivity factor A22, uracil DNA glycosylase E4, and phosphoprotein H5. ...The DNA replication of mpox virus is performed by the viral polymerase F8 and also requires other viral factors, including processivity factor A22, uracil DNA glycosylase E4, and phosphoprotein H5. However, the molecular roles of these viral factors remain unclear. Here, we characterize the structures of F8-A22-E4 and F8-A22-E4-H5 complexes in the presence of different primer-template DNA substrates. E4 is located upstream of F8 on the template single-stranded DNA (ssDNA) and is catalytically active, highlighting a functional coupling between DNA base-excision repair and DNA synthesis. Moreover, H5, in the form of tetramer, binds to the double-stranded DNA (dsDNA) region downstream of F8 in a similar position as PCNA (proliferating cell nuclear antigen) does in eukaryotic polymerase complexes. Omission of H5 or disruption of its DNA interaction showed a reduced synthesis of full-length DNA products. These structures provide snapshots for the working cycle of the polymerase and generate insights into the mechanisms of these essential factors in viral DNA replication. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37722.map.gz | 10.2 MB | EMDB map data format | |
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Header (meta data) | emd-37722-v30.xml emd-37722.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
Images | emd_37722.png | 119.3 KB | ||
Masks | emd_37722_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-37722.cif.gz | 7 KB | ||
Others | emd_37722_half_map_1.map.gz emd_37722_half_map_2.map.gz | 80.9 MB 80.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37722 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37722 | HTTPS FTP |
-Validation report
Summary document | emd_37722_validation.pdf.gz | 707.3 KB | Display | EMDB validaton report |
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Full document | emd_37722_full_validation.pdf.gz | 706.9 KB | Display | |
Data in XML | emd_37722_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_37722_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37722 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37722 | HTTPS FTP |
-Related structure data
Related structure data | 8wppMC 8wpeC 8wpfC 8wpkC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37722.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_37722_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37722_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37722_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : F8-A22-E4-H5 with endogenous DNA
Entire | Name: F8-A22-E4-H5 with endogenous DNA |
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Components |
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-Supramolecule #1: F8-A22-E4-H5 with endogenous DNA
Supramolecule | Name: F8-A22-E4-H5 with endogenous DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: F8-A22-E4-H5
Supramolecule | Name: F8-A22-E4-H5 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Monkeypox virus |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: DNA polymerase
Macromolecule | Name: DNA polymerase / type: protein_or_peptide / ID: 1 / Details: GenBank: URK20494.1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Monkeypox virus |
Molecular weight | Theoretical: 117.147102 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDVRCINWFE SHGENRFLYL KSRCRNGETV FIRFPHYFYY VVTDEIYQSL SPPPFNARPM GKMRTIDIDE TISYNLDIKD RKCSVADMW LIEEPKKRSI QNATMDEFFN ISWFYISNGI SPDGCYSLDE QYLTKINNGC YHCDDPRNCF AKEIPRFDIP R SYLFLDIE ...String: MDVRCINWFE SHGENRFLYL KSRCRNGETV FIRFPHYFYY VVTDEIYQSL SPPPFNARPM GKMRTIDIDE TISYNLDIKD RKCSVADMW LIEEPKKRSI QNATMDEFFN ISWFYISNGI SPDGCYSLDE QYLTKINNGC YHCDDPRNCF AKEIPRFDIP R SYLFLDIE CHFDKKFPSV FINPISHTSY CYIDLSGKRL LFTLINEEML TEQEIQEAVD RGCLRIQSLM EMDYERELVL CS EIVLLRI AKQLLELTFD YVVTFNGHNF DLRYITNRLE LLTGEKIIFR SPDKKEAVHL CIYERNQSSH KGVCGMANTT FHV NNNNGT IFFDLYSFIQ KSEKLDSYKL DSISKNAFSC MGKVLNRGVR EMTFIGDDTT DAKGKADTFA KVLTTGNYVT VDED IICKV IRKDILENGF KVVLSCPTLP NDIYKLSFGK DDIDLAQMYK DYNLNIALDM ARYCIHDACL CQYLWEYYGV ETKTD AGAA TYVLPQSMVF EYRASTIIKG PLLKLLLETK TILVRSETKQ KFPYEGGKVF APKQKMFSNN VLIFDYNSLY PNVCIF GNL SPETLVGVVV STNRLEEEIN NQLLLQKYPP PRYITVHCEP RLPNLISEIA IFDRSIEGTI PRLLRTFLAE RARYKKM LK QATSSTEKAI YDSMQYTYKI VANSVYGLMG FRNSALYSYA SAKSCTSIGR RMILYLESVL NGAELSNGML RFANTLSN P FYMDDRDINP IVKTSLPIDY RFRFRSVYGD TDSVFTEIDS QDVDKSIEIA KELERLINSR VLFNNFKIEF EAVYKNLIM QSKKKYTTMK YSASSNSKSV PERINKGTSE TRRDVSKFHK NMIKTYKTRL SEMLSEGRMN SNQVCIDILR SLETDLRSEF DSRSSPLEL FMLSRMHHSN YKSADNPNMY LVTEYNKNNP ETIELGERYY FAYICPANVP WTKKLVNIKT YETIIDRSFK L GSNQRIFY EVYFKRLTSE IVNLLDNKVL CISFFQRMFG SRPTFYEA |
-Macromolecule #2: A22R DNA polymerase processivity factor
Macromolecule | Name: A22R DNA polymerase processivity factor / type: protein_or_peptide / ID: 2 / Details: GenBank: URK20570.1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Monkeypox virus |
Molecular weight | Theoretical: 50.466277 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MHHHHHHGTG SMTSSADLTN LKELLSLYKS LRFSDSVAIE KYNSLVEWGT STYWKIGVQK VTNVETSISD YYDEVKNKPF NIDPGYYIF LPVYFGSVFI YSKGKNMVEL GSGNSFQIPD EIRSACNKVL DSDNGIDFLR FVLLNNRWIM EDAISKYQSP V NIFKLASE ...String: MHHHHHHGTG SMTSSADLTN LKELLSLYKS LRFSDSVAIE KYNSLVEWGT STYWKIGVQK VTNVETSISD YYDEVKNKPF NIDPGYYIF LPVYFGSVFI YSKGKNMVEL GSGNSFQIPD EIRSACNKVL DSDNGIDFLR FVLLNNRWIM EDAISKYQSP V NIFKLASE YGLNIPNYLE IEIEEDTLFD DELYSIMERS FDDTFPKISI SYIKLGELKR QVVDFFKFSF MYIESIKVDR IG DNIFIPS VITKSGKKIL VKDVDHLIRS KVREHTFVKV KKKNTFSILY DYDGNGTETR GEVIKRIIDT IGRDYYVNGK YFS KVGIAG LKQLTNKLDI NECATVDELV DEINKSGTVK RKIKNQSVFD LSRECLGYPE ADFITLVNNM RFKIENCKVV NFNI ENTNC LNNPSIETIY GNFNQFVSIF NTVTDVKKRL FE |
-Macromolecule #3: E4R Uracil-DNA glycosylase, DNA polymerase processivity factor
Macromolecule | Name: E4R Uracil-DNA glycosylase, DNA polymerase processivity factor type: protein_or_peptide / ID: 3 / Details: GenBank: URK20538.1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Monkeypox virus |
Molecular weight | Theoretical: 25.107742 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 |
-Macromolecule #4: H5R late gene transcription factor
Macromolecule | Name: H5R late gene transcription factor / type: protein_or_peptide / ID: 4 / Details: GenBank: URK20532.1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Monkeypox virus |
Molecular weight | Theoretical: 23.107074 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAWSITNKAD TSSFTKMAEI RAHLRNSAEN KDKNEDIFPE DVIIPSTKPK TKRTTTPRKP AATKRSTKKD KEKEEVEEVV IEEYHQTTE ENSPPPSSSP GVGDIVESVA AVELDDSDGD DEPMVQVEAG KVNHSARSDL SDLKVATDNI VKDLKKIITR I SAVSTVLE ...String: MAWSITNKAD TSSFTKMAEI RAHLRNSAEN KDKNEDIFPE DVIIPSTKPK TKRTTTPRKP AATKRSTKKD KEKEEVEEVV IEEYHQTTE ENSPPPSSSP GVGDIVESVA AVELDDSDGD DEPMVQVEAG KVNHSARSDL SDLKVATDNI VKDLKKIITR I SAVSTVLE DVQAAGISRQ FTSMTKAITT LSDLVTEGKS KVVRKKVKTC KK |
-Macromolecule #5: Primer DNA
Macromolecule | Name: Primer DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.802956 KDa |
Sequence | String: (DA)(DT)(DT)(DT)(DC)(DG)(DC)(DG)(DG)(DG) (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 #6: Template DNA
Macromolecule | Name: Template DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.73649 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)(DC) (DC) (DC)(DG)(DC)(DG)(DA)(DA)(DA)(DT) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-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: 59.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1411000 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |