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- PDB-7yx3: Structure of the Mimivirus genomic fibre in its compact 6-start h... -

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Basic information

Entry
Database: PDB / ID: 7yx3
TitleStructure of the Mimivirus genomic fibre in its compact 6-start helix form
ComponentsPutative GMC-type oxidoreductase
KeywordsVIRAL PROTEIN / Mimivirus / Genomic fibre / Cytoplasmic infectious cycle / 1.2 Mb dsDNA / VIRUS
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / GMC-type oxidoreductase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å
AuthorsVillalta, A. / Schmitt, A. / Estrozi, L.F. / Quemin, E.R.J. / Alempic, J.M. / Lartigue, A. / Prazak, V. / Belmudes, L. / Vasishtan, D. / Colmant, A.M.G. ...Villalta, A. / Schmitt, A. / Estrozi, L.F. / Quemin, E.R.J. / Alempic, J.M. / Lartigue, A. / Prazak, V. / Belmudes, L. / Vasishtan, D. / Colmant, A.M.G. / Honore, F.A. / Coute, Y. / Grunewald, K. / Abergel, C.
Funding supportEuropean Union, France, Germany, United Kingdom, 7items
OrganizationGrant numberCountry
European Research Council (ERC)832601European Union
Agence Nationale de la Recherche (ANR)ANR-16-CE11-0033-01 France
German Research Foundation (DFG)INST 152/772-1|152/774-1|152/775-1|152/776-1 Germany
Wellcome Trust107806/Z/15/Z United Kingdom
German Federal Ministry for Education and Research05K18BHA Germany
Alexander von Humboldt FoundationFRA 1200789 HFST-P Germany
Agence Nationale de la Recherche (ANR)ANR-10-INBS-04 France
CitationJournal: 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
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 2.0Jul 12, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / em_software ...atom_site / em_software / pdbx_contact_author / pdbx_struct_assembly / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_torsion / refine_ls_restr / software / struct_conf / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_assembly.oligomeric_details / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length
Description: Model orientation/position / Provider: author / Type: Coordinate replacement
Revision 2.1Jul 19, 2023Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 2.2Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative GMC-type oxidoreductase
B: Putative GMC-type oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,6074
Polymers154,0362
Non-polymers1,5712
Water00
1
A: Putative GMC-type oxidoreductase
B: Putative GMC-type oxidoreductase
hetero molecules
x 9


Theoretical massNumber of molelcules
Total (without water)1,400,46436
Polymers1,386,32418
Non-polymers14,14018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation8

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Components

#1: Protein Putative GMC-type oxidoreductase


Mass: 77018.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acanthamoeba polyphaga mimivirus / References: UniProt: A0A8A5IZP6
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Mimivirus genomic fibre in its compact 6-start helix form
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Acanthamoeba polyphaga mimivirus / Strain: Reunion
Buffer solutionpH: 7.5
Buffer componentConc.: 40 mM / Name: Tris buffer / Formula: (HOCH2)3CNH2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50.6 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 49.43 ° / Axial rise/subunit: 20.47 Å / Axial symmetry: C3
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 8479 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00610380
ELECTRON MICROSCOPYf_angle_d0.69414178
ELECTRON MICROSCOPYf_dihedral_angle_d5.2071428
ELECTRON MICROSCOPYf_chiral_restr0.0451572
ELECTRON MICROSCOPYf_plane_restr0.0041844

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