[English] 日本語
Yorodumi- EMDB-11095: Masked cryo-EM map of La Crosse virus polymerase cap-binding doma... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11095 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Masked cryo-EM map of La Crosse virus polymerase cap-binding domain and mid domain | |||||||||
Map data | Masked cryo-EM map of La Crosse virus polymerase cap-binding domain and mid domain | |||||||||
Sample |
| |||||||||
Biological species | La Crosse orthobunyavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.54 Å | |||||||||
Authors | Arragain B / Effantin G / Schoehn G / Cusack S / Malet H | |||||||||
Funding support | France, 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational changes. Authors: Benoît Arragain / Grégory Effantin / Piotr Gerlach / Juan Reguera / Guy Schoehn / Stephen Cusack / Hélène Malet / Abstract: Bunyavirales is an order of segmented negative-strand RNA viruses comprising several life-threatening pathogens against which no effective treatment is currently available. Replication and ...Bunyavirales is an order of segmented negative-strand RNA viruses comprising several life-threatening pathogens against which no effective treatment is currently available. Replication and transcription of the RNA genome constitute essential processes performed by the virally encoded multi-domain RNA-dependent RNA polymerase. Here, we describe the complete high-resolution cryo-EM structure of La Crosse virus polymerase. It reveals the presence of key protruding C-terminal domains, notably the cap-binding domain, which undergoes large movements related to its role in transcription initiation, and a zinc-binding domain that displays a fold not previously observed. We capture the polymerase structure at pre-initiation and elongation states, uncovering the coordinated movement of the priming loop, mid-thumb ring linker and lid domain required for the establishment of a ten-base-pair template-product RNA duplex before strand separation into respective exit tunnels. These structural details and the observed dynamics of key functional elements will be instrumental for structure-based development of polymerase inhibitors. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11095.map.gz | 1.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11095-v30.xml emd-11095.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_11095.png | 168.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11095 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11095 | HTTPS FTP |
-Validation report
Summary document | emd_11095_validation.pdf.gz | 199.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_11095_full_validation.pdf.gz | 198.5 KB | Display | |
Data in XML | emd_11095_validation.xml.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11095 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11095 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_11095.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Masked cryo-EM map of La Crosse virus polymerase cap-binding domain and mid domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.826 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : La Crosse virus polymerase cap-binding domain and mid domain
Entire | Name: La Crosse virus polymerase cap-binding domain and mid domain |
---|---|
Components |
|
-Supramolecule #1: La Crosse virus polymerase cap-binding domain and mid domain
Supramolecule | Name: La Crosse virus polymerase cap-binding domain and mid domain type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Masked cryo-EM map of La Crosse virus full-length polymerase, displaying only the cap-binding domain and the mid domain. Masking, 3D classification and refinement enable to obtain a ...Details: Masked cryo-EM map of La Crosse virus full-length polymerase, displaying only the cap-binding domain and the mid domain. Masking, 3D classification and refinement enable to obtain a structure of the cap-binding domain. |
---|---|
Source (natural) | Organism: La Crosse orthobunyavirus |
Molecular weight | Theoretical: 265 KDa |
-Macromolecule #1: La Crosse virus polymerase cap-binding domain and mid domain
Macromolecule | Name: La Crosse virus polymerase cap-binding domain and mid domain type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase |
---|---|
Source (natural) | Organism: La Crosse orthobunyavirus |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGHHHHHHDY DIPTTENLYF QGMDYQEYQQ FLARINTARD ACVAKDIDVD LLMARHDYFG RELCKSLNIE YRNDVPFIDI ILDIRPEVDP LTIDAPHITP DNYLYINNVL YIIDYKVSVS NESSVITYDK YYELTRDISD RLSIPIEIVI IRIDPVSRDL HINSDRFKEL ...String: MGHHHHHHDY DIPTTENLYF QGMDYQEYQQ FLARINTARD ACVAKDIDVD LLMARHDYFG RELCKSLNIE YRNDVPFIDI ILDIRPEVDP LTIDAPHITP DNYLYINNVL YIIDYKVSVS NESSVITYDK YYELTRDISD RLSIPIEIVI IRIDPVSRDL HINSDRFKEL YPTIVVDINF NQFFDLKQLL YEKFGDDEEF LLKVAHGDFT LTAPWCKTGC PEFWKHPIYK EFKMSMPVPE RRLFEESVKF NAYESERWNT NLVKIREYTK KDYSEHISKS AKNIFLASGF YKQPNKNEIS EGWTLMVERV QDQREISKSL HDQKPSIHFI WGAHNPGNSN NATFKLILLS KSLQSIKGIS TYTEAFKSLG KMMDIGDKAI EYEEFCMSLK SKARSSWKQI MNKKLEPKQI NNALVLWEQQ FMINNDLIDK SEKLKLFKNF CGIGKHKQFK NKMLEDLEVS KPKILDFDDA NMYLASLTMM EQSKKILSKS NGLKPDNFIL NEFGSRIKDA NKETYDNMHK IFETGYWQCI SDFSTLMKNI LSVSQYNRHN TFRIAMCANN NVFAIVFPSA DIKTKKATVV YSIIVLHKEE ENIFNPGCLH GTFKCMNGYI SISRAIRLDK ERCQRIVSSP GLFLTTCLLF KHDNPTLVMS DIMNFSIYTS LSITKSVLSL TEPARYMIMN SLAISSNVKD YIAEKFSPYT KTLFSVYMTR LIKNACFDAY DQRQRVQLRD IYLSDYDITQ KGIKDNRELT SIWFPGSVTL KEYLTQIYLP FYFNAKGLHE KHHVMVDLAK TILEIECEQR ENIKEIWSTN CTKQTVNLKI LIHSLCKNLL ADTSRHNHLR NRIENRNNFR RSITTISTFT SSKSCLKIGD FRKEKELQSV KQKKILEVQS RKMRLANPMF VTDEQVCLEV GHCNYEMLRN AMPNYTDYIS TKVFDRLYEL LDKKVLTDKP VIEQIMDMMI DHKKFYFTFF NKGQKTSKDR EIFVGEYEAK MCMYAVERIA KERCKLNPDE MISEPGDGKL KVLEQKSEQE IRFLVETTRQ KNREIDEAIE ALATEGYESN LGKIEKLSLG KAKGLKMEIN ADMSKWSAQD VFYKYFWLIA LDPILYPQEK ERILYFMCNY MDKELILPDE LLFNLLDQKV AYQNDIIATM TNQLNSNTVL IKRNWLQGNF NYTSSYVHSC AMSVYKEILK EAITLLDGSI LVNSLVHSDD NQTSITIVQD KMENDKIIDF AMKEFERACL TFGCQANMKK TYVTNCIKEF VSLFNLYGEP FSIYGRFLLT SVGDCAYIGP YEDLASRISS AQTAIKHGCP PSLAWVSIAI SHWMTSLTYN MLPGQSNDPI DYFPAENRKD IPIELNGVLD APLSMISTVG LESGNLYFLI KLLSKYTPVM QKRESVVNQI AEVKNWKVED LTDNEIFRLK ILRYLVLDAE MDPSDIMGET SDMRGRSILT PRKFTTAGSL RKLYSFSKYQ DRLSSPGGMV ELFTYLLEKP ELLVTKGEDM KDYMESVIFR YNSKRFKESL SIQNPAQLFI EQILFSHKPV IDFSGIRDKY INLHDSRALE KEPDILGKVT FTEAYRLLMR DLSSLELTND DIQVIYSYII LNDPMMITIA NTHILSIYGS PQRRMGMSCS TMPEFRNLKL IHHSPALVLR AYSKNNPDIQ GADPTEMARD LVHLKEFVEN TNLEEKMKVR IAMNEAEKGQ RDIVFELKEM TRFYQVCYEY VKSTEHKIKV FILPAKSYTT TDFCSLMQGN LIKDKEWYTV HYLKQILSGG HKAIMQHNAT SEQNIAFECF KLITHFADSF IDSLSRSAFL QLIIDEFSYK DVKVSKLYDI IKNGYNRTDF IPLLFRTGDL RQADLDKYDA MKSHERVTWN DWQTSRHLDM GSINLTITGY NRSITIIGED NKLTYAELCL TRKTPENITI SGRKLLGSRH GLKFENMSKI QTYPGNYYIT YRKKDRHQFV YQIHSHESIT RRNEEHMAIR TRIYNEITPV CVVNVAEVDG DQRILIRSLD YLNNDIFSLS RIKVGLDEFA TIKKAHFSKM VSFEGPPIKT GLLDLTELMK SQDLLNLNYD NIRNSNLISF SKLICCEGSD NINDGLEFLS DDPMNFTEGE AIHSTPIFNI YYSKRGERHM TYRNAIKLLI ERETKIFEEA FTFSENGFIS PENLGCLEAV VSLIKLLKTN EWSTVIDKCI HICLIKNGMD HMYHSFDVPK CFMGNPITRD INWVMFREFI NSLPGTDIPP WNVMTENFKK KCIALINSKF ETQRDFSEFT KLMKKEGGRS NIEFD |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||
---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
Details: 20 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM TCEP | ||||||||
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: 30mA | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV / Details: blot time: 2 sec, blot force: 1. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Min: 90.0 K / Max: 90.0 K |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 16498 / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.5 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
---|