+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13641 | ||||||||||||||||||||||||
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Title | Structure of the Mimivirus genomic fibre asymmetric unit | ||||||||||||||||||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||||||||
Authors | Villalta A / Schmitt A / Estrozi LF / Quemin ERJ / Alempic JM / Lartigue A / Prazak V / Belmudes L / Vasishtan D / Colmant AMG ...Villalta A / Schmitt A / Estrozi LF / Quemin ERJ / Alempic JM / Lartigue A / Prazak V / Belmudes L / Vasishtan D / Colmant AMG / Honore FA / Coute Y / Grunewald K / Abergel C | ||||||||||||||||||||||||
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_13641.map.gz | 4 MB | EMDB map data format | |
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Header (meta data) | emd-13641-v30.xml emd-13641.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13641_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_13641.png | 71.9 KB | ||
Masks | emd_13641_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-13641.cif.gz | 6.1 KB | ||
Others | emd_13641_additional_1.map.gz emd_13641_half_map_1.map.gz emd_13641_half_map_2.map.gz | 49.3 MB 49.5 MB 49.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13641 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13641 | HTTPS FTP |
-Validation report
Summary document | emd_13641_validation.pdf.gz | 759.8 KB | Display | EMDB validaton report |
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Full document | emd_13641_full_validation.pdf.gz | 759.4 KB | Display | |
Data in XML | emd_13641_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | emd_13641_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13641 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13641 | HTTPS FTP |
-Related structure data
Related structure data | 7ptvMC 7yx3C 7yx4C 7yx5C 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_13641.map.gz / Format: CCP4 / Size: 64 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
-Mask #1
File | emd_13641_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Map before postprocessing
File | emd_13641_additional_1.map | ||||||||||||
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Annotation | Map before postprocessing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13641_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13641_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structure of the Mimivirus genomic fibre asymmetric unit
Entire | Name: Structure of the Mimivirus genomic fibre asymmetric unit |
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Components |
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-Supramolecule #1: Structure of the Mimivirus genomic fibre asymmetric unit
Supramolecule | Name: Structure of the Mimivirus genomic fibre asymmetric unit type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Acanthamoeba polyphaga mimivirus / Strain: Reunion |
-Macromolecule #1: Putative glucose-methanol-choline oxidoreductase protein
Macromolecule | Name: Putative glucose-methanol-choline oxidoreductase protein 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: 76.431055 KDa |
Sequence | String: MAHRSRCNCN DTSNSNGSQH GINLPLRKID TYDPCVNCRV KPHLCPKPHP CPKPENLEAD IVIIGAGAAG CVLAYYLTKF SDLKIILLE AGHTHFNDPV VTDPMGFFGK YNPPNENIRM SQNPSYAWQP ALEPDTGAYS MRNVVAHGLA VGGSTAINQL N YIVGGRTV ...String: MAHRSRCNCN DTSNSNGSQH GINLPLRKID TYDPCVNCRV KPHLCPKPHP CPKPENLEAD IVIIGAGAAG CVLAYYLTKF SDLKIILLE AGHTHFNDPV VTDPMGFFGK YNPPNENIRM SQNPSYAWQP ALEPDTGAYS MRNVVAHGLA VGGSTAINQL N YIVGGRTV FDNDWPTGWK YDDIKKYFRR VLADISPIRD GTKVNLTNTI LESMRVLADQ QVSSGVPVDF LINKATGGLP NI EQTYQGA PIVNLNDYEG INSVCGFKSY YVGVNQLSDG SYIRKYAGNT YLNSYYVDSN GFGIGKFSNL RVISDAVVDR IHF EGQRAV SVTYIDKKGN LHSVKVHKEV EICSGSFFTP TILQRSGIGD FSYLSSIGVP DLVYNNPLVG QGLRNHYSPI TQVS VTGPD AAAFLSNTAA GPTNMSFRGA GMLGYHKLEP NKPSNAGSVT YRKYELLVTG GVAISADQQY LSGISSSTGN YFALI ADDI RFAPVGYIKI GTPNFPRDTP KIFFNTFVNY TPTTDPADQQ WPVAQKTLAP LISALLGYDA IYQIVQQMKV VAVNAG FNV TLQMAYPPND LLVELHNGLN TYGINWWHYF VPSLVNDDTP AGKLFASTLS KLSYYPRSGA HLDSHQSCSC SIGGTVD TE LKVIGVENVR VTDLSAAPHP PGGNTWCTAA MIGARATDLI LGKPLVANLP PEDVPVFTTS UniProtKB: Putative glucose-methanol-choline oxidoreductase protein |
-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 | single particle reconstruction |
Aggregation state | particle |
-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 |