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- EMDB-29290: Nodavirus RNA replication proto-crown, detergent-solubliized C11 ... -
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Open data
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Basic information
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Title | Nodavirus RNA replication proto-crown, detergent-solubliized C11 multimer | |||||||||
![]() | Nodavirus RNA replication proto-crown, detergent-solubilized C11 multimer. | |||||||||
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Function / homology | Nodavirus methyltransferase domain / Nodavirus Vmethyltransferase / host cell mitochondrial outer membrane / ![]() ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Zhan H / Unchwaniwala N / Rebolledo Viveros A / Pennington J / Horswill M / Broadberry R / Myers J / den Boon J / Grant T / Ahlquist P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Nodavirus RNA replication crown architecture reveals proto-crown precursor and viral protein A conformational switching. Authors: Hong Zhan / Nuruddin Unchwaniwala / Andrea Rebolledo-Viveros / Janice Pennington / Mark Horswill / Roma Broadberry / Jonathan Myers / Johan A den Boon / Timothy Grant / Paul Ahlquist / ![]() Abstract: Positive-strand RNA viruses replicate their genomes in virus-induced membrane vesicles, and the resulting RNA replication complexes are a major target for virus control. Nodavirus studies first ...Positive-strand RNA viruses replicate their genomes in virus-induced membrane vesicles, and the resulting RNA replication complexes are a major target for virus control. Nodavirus studies first revealed viral RNA replication proteins forming a 12-fold symmetric "crown" at the vesicle opening to the cytosol, an arrangement recently confirmed to extend to distantly related alphaviruses. Using cryoelectron microscopy (cryo-EM), we show that mature nodavirus crowns comprise two stacked 12-mer rings of multidomain viral RNA replication protein A. Each ring contains an ~19 nm circle of C-proximal polymerase domains, differentiated by strikingly diverged positions of N-proximal RNA capping/membrane binding domains. The lower ring is a "proto-crown" precursor that assembles prior to RNA template recruitment, RNA synthesis, and replication vesicle formation. In this proto-crown, the N-proximal segments interact to form a toroidal central floor, whose 3.1 Å resolution structure reveals many mechanistic details of the RNA capping/membrane binding domains. In the upper ring, cryo-EM fitting indicates that the N-proximal domains extend radially outside the polymerases, forming separated, membrane-binding "legs." The polymerase and N-proximal domains are connected by a long linker accommodating the conformational switch between the two rings and possibly also polymerase movements associated with RNA synthesis and nonsymmetric electron density in the lower center of mature crowns. The results reveal remarkable viral protein multifunctionality, conformational flexibility, and evolutionary plasticity and insights into (+)RNA virus replication and control. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 677.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.6 KB 18.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.2 KB | Display | ![]() |
Images | ![]() | 202.9 KB | ||
Others | ![]() ![]() | 675 MB 675 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fmaMC ![]() 8fm9C ![]() 8fmbC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Nodavirus RNA replication proto-crown, detergent-solubilized C11 multimer. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.833 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Nodavirus RNA replication proto-crown, detergent-solubilized C11 multimer, unmasked...
File | emd_29290_half_map_1.map | ||||||||||||
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Annotation | Nodavirus RNA replication proto-crown, detergent-solubilized C11 multimer, unmasked and unfiltered half map1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Nodavirus RNA replication proto-crown, detergent-solubilized C11 multimer, unmasked...
File | emd_29290_half_map_2.map | ||||||||||||
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Annotation | Nodavirus RNA replication proto-crown, detergent-solubilized C11 multimer, unmasked and unfiltered half map2. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Nodavirus RNA replication proto-crown, detergent-solubliized C11 ...
Entire | Name: Nodavirus RNA replication proto-crown, detergent-solubliized C11 multimer |
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Components |
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-Supramolecule #1: Nodavirus RNA replication proto-crown, detergent-solubliized C11 ...
Supramolecule | Name: Nodavirus RNA replication proto-crown, detergent-solubliized C11 multimer type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: RNA-directed RNA polymerase
Macromolecule | Name: RNA-directed RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 113.996586 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MTLKVILGEH QITRTELLVG IATVSGCGAV VYCISKFWGY GAIAPYPQSG GNRVTRALQR AVIDKTKTPI ETRFYPLDSL RTVTPKRVA DNGHAVSGAV RDAARRLIDE SITAVGGSKF EVNPNPNSST GLRNHFHFAV GDLAQDFRND TPADDAFIVG V DVDYYVTE ...String: MTLKVILGEH QITRTELLVG IATVSGCGAV VYCISKFWGY GAIAPYPQSG GNRVTRALQR AVIDKTKTPI ETRFYPLDSL RTVTPKRVA DNGHAVSGAV RDAARRLIDE SITAVGGSKF EVNPNPNSST GLRNHFHFAV GDLAQDFRND TPADDAFIVG V DVDYYVTE PDVLLEHMRP VVLHTFNPKK VSGFDADSPF TIKNNLVEYK VSGGAAWVHP VWDWCEAGEF IASRVRTSWK EW FLQLPLR MIGLEKVGYH KIHHCRPWTD CPDRALVYTI PQYVIWRFNW IDTELHVRKL KRIEYQDETK PGWNRLEYVT DKN ELLVSI GREGEHAQIT IEKEKLDMLS GLSATQSVNA RLIGMGHKDP QYTSMIVQYY TGKKVVSPIS PTVYKPTMPR VHWP VTSDA DVPEVSARQY TLPIVSDCMM MPMIKRWETM SESIERRVTF VANDKKPSDR IAKIAETFVK LMNGPFKDLD PLSIE ETIE RLNKPSQQLQ LRAVFEMIGV KPRQLIESFN KNEPGMKSSR IISGFPDILF ILKVSRYTLA YSDIVLHAEH NEHWYY PGR NPTEIADGVC EFVSDCDAEV IETDFSNLDG RVSSWMQRNI AQKAMVQAFR PEYRDEIISF MDTIINCPAK AKRFGFR YE PGVGVKSGSP TTTPHNTQYN GCVEFTALTF EHPDAEPEDL FRLIGPKCGD DGLSRAIIQK SINRAAKCFG LELKVERY N PEIGLCFLSR VFVDPLATTT TIQDPLRTLR KLHLTTRDPT IPLADAACDR VEGYLCTDAL TPLISDYCKM VLRLYGPTA STEQVRNQRR SRNKEKPYWL TCDGSWPQHP QDAHLMKQVL IKRTAIDEDQ VDALIGRFAA MKDVWEKITH DSEESAAACT FDEDGVAPN SVDESLPLLN DAKQTRANPG TSRPHSNGGG SSHGNELPRR TEQRAQGPRQ PARLPKQGKT NGKSDGNITA G ETQRGGIP RGKGPRGGKT NTRRTPPKAG AQPQPSNNRK SRLEEELRRR LTE |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2.0 nm |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 100.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | The final model includes 22 chains representing 11 protein A polypeptides. Chains A-K represent the N-terminal floor segment built into the high-resolution EM density. Chains L-V represent a mainchain trace of the polymerase segment rigid body fit into the map and are included to give a more complete picture of the molecule. The polymerase mainchain trace was refined from an Alphafold prediction into a map obtained by symmetry expansion with subtraction. The polymerase map is uploaded as a separate entry. The two segments have separate chain IDs as it is unclear from the density which polymerase connects to which floor segment. |
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Refinement | Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-8fma: |