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Yorodumi- EMDB-14353: Structure of the Mimivirus genomic fibre in its compact 6-start h... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14353 | ||||||||||||||||||||||||
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Title | Structure of the Mimivirus genomic fibre in its compact 6-start helix form | ||||||||||||||||||||||||
Map data | postprocessed masked map | ||||||||||||||||||||||||
Sample |
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Keywords | Mimivirus / Genomic fibre / Cytoplasmic infectious cycle / 1.2 Mb dsDNA / VIRUS / VIRAL PROTEIN | ||||||||||||||||||||||||
Function / homology | Function and homology information choline dehydrogenase activity / glycine betaine biosynthetic process from choline / flavin adenine dinucleotide binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | Acanthamoeba polyphaga mimivirus | ||||||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||||||||||||||
Authors | Villalta A / Schmitt A | ||||||||||||||||||||||||
Funding support | European Union, France, Germany, United Kingdom, 7 items
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Citation | Journal: Elife / Year: 2022 Title: The giant mimivirus 1.2 Mb genome is elegantly organized into a 30-nm diameter helical protein shield. Authors: Alejandro Villalta / Alain Schmitt / Leandro F Estrozi / Emmanuelle R J Quemin / Jean-Marie Alempic / Audrey Lartigue / Vojtěch Pražák / Lucid Belmudes / Daven Vasishtan / Agathe M G ...Authors: Alejandro Villalta / Alain Schmitt / Leandro F Estrozi / Emmanuelle R J Quemin / Jean-Marie Alempic / Audrey Lartigue / Vojtěch Pražák / Lucid Belmudes / Daven Vasishtan / Agathe M G Colmant / Flora A Honoré / Yohann Couté / Kay Grünewald / Chantal Abergel / Abstract: Mimivirus is the prototype of the family of giant dsDNA viruses. Little is known about the organization of the 1.2 Mb genome inside the membrane-limited nucleoid filling the ~0.5 µm icosahedral ...Mimivirus is the prototype of the family of giant dsDNA viruses. Little is known about the organization of the 1.2 Mb genome inside the membrane-limited nucleoid filling the ~0.5 µm icosahedral capsids. Cryo-electron microscopy, cryo-electron tomography, and proteomics revealed that it is encased into a ~30-nm diameter helical protein shell surprisingly composed of two GMC-type oxidoreductases, which also form the glycosylated fibrils decorating the capsid. The genome is arranged in 5- or 6-start left-handed super-helices, with each DNA-strand lining the central channel. This luminal channel of the nucleoprotein fiber is wide enough to accommodate oxidative stress proteins and RNA polymerase subunits identified by proteomics. Such elegant supramolecular organization would represent a remarkable evolutionary strategy for packaging and protecting the genome, in a state ready for immediate transcription upon unwinding in the host cytoplasm. The parsimonious use of the same protein in two unrelated substructures of the virion is unexpected for a giant virus with thousand genes at its disposal. | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14353.map.gz | 30.2 MB | EMDB map data format | |
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Header (meta data) | emd-14353-v30.xml emd-14353.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14353_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_14353.png | 85.2 KB | ||
Filedesc metadata | emd-14353.cif.gz | 6.1 KB | ||
Others | emd_14353_additional_1.map.gz emd_14353_half_map_1.map.gz emd_14353_half_map_2.map.gz | 193.6 MB 193.9 MB 193.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14353 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14353 | HTTPS FTP |
-Validation report
Summary document | emd_14353_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_14353_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_14353_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | emd_14353_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14353 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14353 | HTTPS FTP |
-Related structure data
Related structure data | 7yx3MC 7ptvC 7yx4C 7yx5C 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_14353.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | postprocessed masked map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unmasked map before postprocessing
File | emd_14353_additional_1.map | ||||||||||||
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Annotation | Unmasked map before postprocessing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unmasked half map
File | emd_14353_half_map_1.map | ||||||||||||
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Annotation | Unmasked half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unmasked half map
File | emd_14353_half_map_2.map | ||||||||||||
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Annotation | Unmasked half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mimivirus genomic fibre in its compact 6-start helix form
Entire | Name: Mimivirus genomic fibre in its compact 6-start helix form |
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Components |
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-Supramolecule #1: Mimivirus genomic fibre in its compact 6-start helix form
Supramolecule | Name: Mimivirus genomic fibre in its compact 6-start helix form type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Acanthamoeba polyphaga mimivirus / Strain: Reunion |
-Macromolecule #1: Putative GMC-type oxidoreductase
Macromolecule | Name: Putative GMC-type oxidoreductase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Acanthamoeba polyphaga mimivirus |
Molecular weight | Theoretical: 77.018023 KDa |
Sequence | String: MKNRECCKCY NPCEKICVNY STTDVAFERP NPCKPTPCKP TPIPCDPCHN TKDNLTGDIV IIGAGAAGSL LAHYLARFSN MKIILLEAG HSHFNDPVVT DPMGFFGKYN PPNENISMSQ NPSYSWQGAQ EPNTGAYGNR PIIAHGMGFG GSTMINRLNL V VGGRTVFD ...String: MKNRECCKCY NPCEKICVNY STTDVAFERP NPCKPTPCKP TPIPCDPCHN TKDNLTGDIV IIGAGAAGSL LAHYLARFSN MKIILLEAG HSHFNDPVVT DPMGFFGKYN PPNENISMSQ NPSYSWQGAQ EPNTGAYGNR PIIAHGMGFG GSTMINRLNL V VGGRTVFD NDWPVGWKYD DVKNYFRRVL VDINPVRDNT KASITSVALD ALRIIAEQQI ASGEPVDFLL NKATGNVPNV EK TTPDAVP LNLNDYEGVN SVVAFSSFYM GVNQLSDGNY IRKYAGNTYL NRNYVDENGR GIGKFSGLRV VSDAVVDRII FKG NRAVGV NYIDREGIMH YVKVNKEVVV TSGAFYTPTI LQRSGIGDFT YLSSIGVKNL VYNNPLVGTG LKNHYSPVTI TRVH GEPSE VSRFLSNMAA NPTNMGFKGL AELGFHRLDP NKPANANTVT YRKYQLMMTA GVGIPAEQQY LSGLSPSSNN LFTLI ADDI RFAPEGYIKI GTPNIPRDVP KIFFNTFVTY TPTSAPADQQ WPIAQKTLAP LISALLGYDI IYQTLISMNQ TARDSG FQV SLEMVYPLND LIYKLHNGLA TYGANWWHYF VPTLVGDDTP AGREFADTLS KLSYYPRVGA HLDSHQGCSC SIGRTVD SN LKVIGTQNVR VADLSAAAFP PGGNTWATAS MIGARAVDLI LGFPYLRDLP VNDVPILNVN UniProtKB: GMC-type oxidoreductase |
-Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 2 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 / Component - Concentration: 40.0 mM / Component - Formula: (HOCH2)3CNH2 / Component - Name: Tris buffer |
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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 K2 QUANTUM (4k x 4k) / Average electron dose: 50.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |