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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM of Hantaan virus polymerase in hexameric state | |||||||||
![]() | HTNV-L Hexamer Apo | |||||||||
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![]() | Bunyavirus / Hantaan virus / polymerase / dimer / VIRAL PROTEIN | |||||||||
Function / homology | ![]() RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / endonuclease activity / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.24 Å | |||||||||
![]() | Durieux Trouilleton Q / Arragain B / Malet H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of the oligomerization of full-length Hantaan virus polymerase into symmetric dimers and hexamers. Authors: Quentin Durieux Trouilleton / Dominique Housset / Paco Tarillon / Benoît Arragain / Hélène Malet / ![]() Abstract: Hantaan virus is a dangerous human pathogen whose segmented negative-stranded RNA genome is replicated and transcribed by a virally-encoded multi-functional polymerase. Here we describe the complete ...Hantaan virus is a dangerous human pathogen whose segmented negative-stranded RNA genome is replicated and transcribed by a virally-encoded multi-functional polymerase. Here we describe the complete cryo-electron microscopy structure of Hantaan virus polymerase in several oligomeric forms. Apo polymerase protomers can adopt two drastically different conformations, which assemble into two distinct symmetric homodimers, that can themselves gather to form hexamers. Polymerase dimerization induces the stabilization of most polymerase domains, including the C-terminal domain that contributes the most to dimer's interface, along with a lariat region that participates to the polymerase steadying. Binding to viral RNA induces significant conformational changes resulting in symmetric oligomer disruption and polymerase activation, suggesting the possible involvement of apo multimers as protecting systems that would stabilize the otherwise flexible C-terminal domains. Overall, these results provide insights into the multimerization capability of Hantavirus polymerase and may help to define antiviral compounds to counteract these life-threatening viruses. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 651.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.2 KB 20.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 23.3 KB | Display | ![]() |
Images | ![]() | 71.3 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() | 1.2 GB 1.2 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qe5C ![]() 8qgtC ![]() 8qguC ![]() 8qh3C ![]() 8qhdC 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
File | ![]() | ||||||||||||||||||||
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Annotation | HTNV-L Hexamer Apo | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.839 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: HTNV-L Hexamer Apo half map A
File | emd_18406_half_map_1.map | ||||||||||||
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Annotation | HTNV-L Hexamer Apo half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: HTNV-L Hexamer Apo half map b
File | emd_18406_half_map_2.map | ||||||||||||
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Annotation | HTNV-L Hexamer Apo half map b | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Hantaan virus polymerase
Entire | Name: Hantaan virus polymerase |
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Components |
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-Supramolecule #1: Hantaan virus polymerase
Supramolecule | Name: Hantaan virus polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.5 MDa |
-Macromolecule #1: Hantaan virus polymerase
Macromolecule | Name: Hantaan virus polymerase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: MGHHHHHHDY DIPTTENLYF QGMDKYREIH NKLKEFSPGT LTAVECIDYL DRLYAVRHDI VDQMIKHDWS DNKDSEEAIG KVLLFAGVPS NIITALEKKI IPNHPTGKSL KAFFKMTPDN YKISGTTIEF VEVTVTADVD KGIREKKLKY EAGLTYIEQE LHKFFLKGEI ...String: MGHHHHHHDY DIPTTENLYF QGMDKYREIH NKLKEFSPGT LTAVECIDYL DRLYAVRHDI VDQMIKHDWS DNKDSEEAIG KVLLFAGVPS NIITALEKKI IPNHPTGKSL KAFFKMTPDN YKISGTTIEF VEVTVTADVD KGIREKKLKY EAGLTYIEQE LHKFFLKGEI PQPYKITFNV VAVRTDGSNI TTQWPSRRND GVVQYMRLVQ AEISYVREHL IKTEERAALE AMFNLKFNIS THKSQPYYIP DYKGMEPIGA NIEDLVDYSK DWLSRARNFS FFEVKGTAVF ECFNSNEANH CQRYPMSRKP RNFLLIQCSL ITSYKPATTL SDQIDSRRAC SYILNLIPDT PASYLIHDMA YRYINLTRED MINYYAPRIQ FKQTQNVREP GTFKLTSSML RAESKAMLDL LNNHKSGEKH GAQIESLNIA SHIVQSESVS LITKILSDLE LNITEPSTQE YSTTKHTYVD TVLDKFFQNE TQKYLIDVLK KTTAWHIGHL IRDITESLIA HSGLKRSKYW SLHSYNNGNV ILFILPSKSL EVAGSFIRFI TVFRIGPGLV DKDNLDTILI DGDSQWGVSK VMSIDLNRLL ALNIAFEKAL IATATWFQYY TEDQGQFPLQ YAIRSVFANH FLLAICQKMK LCAIFDNLRY LIPAVTSLYS GFPSLIEKLF ERPFKSSLEV YIYYNIKSLL VALAQNNKAR FYSKVKLLGL TVDQSTVGAS GVYPSFMSRI VYKHYRSLIS EVTTCFFLFE KGLHGNMNEE AKIHLETVEW ALKFREKEEK YGESLVENGY MMWELRANAE LAEQQLYCQD AIELAAIELN KVLATKSSVV ANSILSKNWE EPYFSQTRNI SLKGMSGQVQ EDGHLSSSVT IIEAIRYLSN SRHNPSLLKL YEETREQKAM ARIVRKYQRT EADRGFFITT LPTRCRLEII EDYYDAIAKN ISEEYISYGG EKKILAIQGA LEKALRWASG ESFIELSNHK FIRMKRKLMY VSADATKWSP GDNSAKFRRF TSMLHNGLPN NKLKNCVIDA LKQVYKTDFF MSRKLRNYID SMESLDPHIK QFLDFFPDGH HGEVKGNWLQ GNLNKCSSLF GVAMSLLFKQ VWTNLFPELD CFFEFAHHSD DALFIYGYLE PVDDGTDWFL FVSQQIQAGH LHWFSVNTEM WKSMFNLHEH ILLLGSIKIS PKKTTVSPTN AEFLSTFFEG CAVSIPFVKI LLGSLSDLPG LGYFDDLAAA QSRCVKALDL GASPQVAQLA VALCTSKVER LYGTAPGMVN HPAAYLQVKH TDTPIPLGGN GAMSIMELAT AGIGMSDKNL LKRALLGYSH KRQKSMLYIL GLFKFLMKLS DETFQHERLG QFSFIGKVQW KIFTPKSEFE FADMYTSKFL ELWSSQHVTY DYIIPKGRDN LLIYLVRKLN DPSIVTAMTM QSPLQLRFRM QAKQHMKVCR LDGEWVTFRE VLAAANSFAE NYSATSQDMD LFQTLTSCTF SKEYAWKDFL NGIHCDVIPT KQVQRAKVAR TFTVREKDQI IQNSIPAVIG YKFAVTVEEM SDVLDTAKFP DSLSVDLKTM KDGVYRELGL DISLPDVMKR IAPMLYKSSK SRVVIVQGNV EGTAEAICRY WLKSMSLVKT IRVKPHKEVL QAVSIFNRKE DIGQQKDLAA LKLCIEVWRW CKANSAPYRD WFQALWFEDK TFSEWLDRFC RVGVPPIDPE IQCAALMIAD IKGDYSVLQL QANRRAYSGK QYDAYCVQTY NEVTKLYEGD LRVTFNFGLD CARLEIFWDK KAYILETSIT QKHVLKIMMD EVSKELIKCG MRFNTEQVQG VRHMVLFKTE SGFEWGKPNI PCIVYKNCVL RTSLRTTQAI NHKFMITIKD DGLRAIAQHD EDSPRFLLAH AFHTIRDIRY QAVDAVSNVW FIHKGVKLYL NPIISSGLLE NFMKNLPAAI PPAAYSLIMN RAKISVDLFM FNDLLKLINP RNTLDLSGLE TTGDEFSTVS SMSSRLWSEE MSLVDDDEEL DDEFTIDLQD VDFENIDIEA DIEHFLQDES SYTGDLLIST EETESKKMRG IVKILEPVRL IKSWVSRGLS IEKVYSPVNI ILMSRYISKT FNLSTKQVSL LDPYDLTELE SIVRGWGECV IDQFESLDRE AQNMVVNKGI CPEDVIPDSL FSFRHTMVLL RRLFPQDSIS SFY UniProtKB: RNA-directed RNA polymerase L |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.25 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR / Details: 25mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 1 3s. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 14650 / Average exposure time: 1.45 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL |