+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38395 | |||||||||
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Title | The Cryo-EM structure of MPXV E5 in complex with DNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | primase / helicase / REPLICATION | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Monkeypox virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.74 Å | |||||||||
Authors | Zhang W / Liu Y / Gao H / Gan J | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Discov / Year: 2024 Title: Structural and functional insights into the helicase protein E5 of Mpox virus. Authors: Gan J / Zhang W | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38395.map.gz | 79 MB | EMDB map data format | |
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Header (meta data) | emd-38395-v30.xml emd-38395.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38395_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_38395.png | 34.5 KB | ||
Filedesc metadata | emd-38395.cif.gz | 5.9 KB | ||
Others | emd_38395_half_map_1.map.gz emd_38395_half_map_2.map.gz | 77.6 MB 77.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38395 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38395 | HTTPS FTP |
-Related structure data
Related structure data | 8xj7MC 8xifC 8xigC 8xj6C 8xj8C M: atomic model generated by this map C: citing same article (ref.) |
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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_38395.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0773 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38395_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38395_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Monkeypox virus
Entire | Name: Monkeypox virus |
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Components |
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-Supramolecule #1: Monkeypox virus
Supramolecule | Name: Monkeypox virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 10244 / Sci species name: Monkeypox virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes |
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-Macromolecule #1: Monkeypox virus E5
Macromolecule | Name: Monkeypox virus E5 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Monkeypox virus |
Molecular weight | Theoretical: 90.476344 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDAAIRGNDV IFVLKTIGVP SACRQNEDPR FVEAFKCDEL ERYIDNNPEC TLFESLRDEE AYSIVRIFMD VDLDACLDEI DYLTAIQDF IIEVSNCVAR FAFTECGAIH ENVIKSMRSN FSLTKSTNRD KTSFHIIFLD TYTTMDTLIA MKRTLLELSR S SENPLTRS ...String: MDAAIRGNDV IFVLKTIGVP SACRQNEDPR FVEAFKCDEL ERYIDNNPEC TLFESLRDEE AYSIVRIFMD VDLDACLDEI DYLTAIQDF IIEVSNCVAR FAFTECGAIH ENVIKSMRSN FSLTKSTNRD KTSFHIIFLD TYTTMDTLIA MKRTLLELSR S SENPLTRS IDTAVYRRKT TLRVVGTRKN PNCDTIHVMQ PPHDNIEDYL FTYVDMNNNS YYFSLQRRLE DLVPDKLWEP GF ISFEDAI KRVSKIFINS IINFNDLDEN NFTTVPLVID YVTPCALCKK RSHKHPHQLS LENGAIRIYK TGNPHSCKVK IVP LDGNKL FNIAQRILDT NSVLLTERGD HIVWINNSWK FNSEEPLITK LILSIRHQLP KEYSSELLCP RKRKTVEANI RDML VDSVE TDTYPDKLPF KNGVLDLVDG MFYSGDDAKK YTCTVSTGFK FDDTKFVEDS PEMEELMNII NDIQPLTDEN KKNRE LYEK TLSSCLCGAT KGCLTFFFGE TATGKSTTKR LLKSAIGDLF VETGQTILTD VLDKGPNPFI ANMHLKRSVF CSELPD FAC SGSKKIRSDN IKKLTEPCVI GRPCFSNKIN NRNHATIIID TNYKPVFDRI DNALMRRIAV VRFRTHFSQP SGREAAE NN DAYDKVKLLD EGLDGKIQNN RYRFAFLYLL VKWYKKYHIP IMKLYPTPEE IPDFAFYLKI GTLLVSSSVK HIPLMTDL S KKGYILYDNV VTLPLTTFQQ KISKYFNSRL FGHDIESFIN RHKKFANVSD EYLQYIFIED ISSP UniProtKB: Uncoating factor OPG117 |
-Macromolecule #2: DNA (70-MER)
Macromolecule | Name: DNA (70-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Monkeypox virus |
Molecular weight | Theoretical: 21.440668 KDa |
Sequence | String: (DA)(DA)(DC)(DG)(DA)(DG)(DT)(DC)(DA)(DA) (DG)(DC)(DG)(DC)(DA)(DT)(DC)(DC)(DC)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT) ...String: (DA)(DA)(DC)(DG)(DA)(DG)(DT)(DC)(DA)(DA) (DG)(DC)(DG)(DC)(DA)(DT)(DC)(DC)(DC)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DC)(DG)(DG)(DG)(DA)(DT)(DG)(DC) (DG)(DC) (DT)(DT)(DG)(DA)(DC)(DT)(DC) (DG)(DT)(DT) |
-Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 6 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-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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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: 2.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |