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Open data
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Basic information
Entry | Database: PDB / ID: 7ojn | |||||||||
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Title | Lassa virus L protein in an elongation conformation [ELONGATION] | |||||||||
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![]() | VIRAL PROTEIN / Lassa virus RNA-dependent RNA polymerase viral RNA | |||||||||
Function / homology | ![]() negative stranded viral RNA replication / cap snatching / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | |||||||||
![]() | Kouba, T. / Vogel, D. / Thorkelsson, S. / Quemin, E. / Williams, H.M. / Milewski, M. / Busch, C. / Gunther, S. / Grunewald, K. / Rosenthal, M. / Cusack, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational changes in Lassa virus L protein associated with promoter binding and RNA synthesis activity. Authors: Tomas Kouba / Dominik Vogel / Sigurdur R Thorkelsson / Emmanuelle R J Quemin / Harry M Williams / Morlin Milewski / Carola Busch / Stephan Günther / Kay Grünewald / Maria Rosenthal / Stephen Cusack / ![]() ![]() Abstract: Lassa virus is endemic in West Africa and can cause severe hemorrhagic fever. The viral L protein transcribes and replicates the RNA genome via its RNA-dependent RNA polymerase activity. Here, we ...Lassa virus is endemic in West Africa and can cause severe hemorrhagic fever. The viral L protein transcribes and replicates the RNA genome via its RNA-dependent RNA polymerase activity. Here, we present nine cryo-EM structures of the L protein in the apo-, promoter-bound pre-initiation and active RNA synthesis states. We characterize distinct binding pockets for the conserved 3' and 5' promoter RNAs and show how full-promoter binding induces a distinct pre-initiation conformation. In the apo- and early elongation states, the endonuclease is inhibited by two distinct L protein peptides, whereas in the pre-initiation state it is uninhibited. In the early elongation state, a template-product duplex is bound in the active site cavity together with an incoming non-hydrolysable nucleotide and the full C-terminal region of the L protein, including the putative cap-binding domain, is well-ordered. These data advance our mechanistic understanding of how this flexible and multifunctional molecular machine is activated. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 393.4 KB | Display | ![]() |
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PDB format | ![]() | 310 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 66.2 KB | Display | |
Data in CIF | ![]() | 99.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12956MC ![]() 7ochC ![]() 7oe3C ![]() 7oe7C ![]() 7oeaC ![]() 7oebC ![]() 7ojjC ![]() 7ojkC ![]() 7ojlC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 1 types, 1 molecules L
#1: Protein | Mass: 253656.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MEDDMACVKDLVSKYLADNERLSRQKLAFLVQTEPRMLLMEGLKLLSLCIEIDSCNANGCEHNSEDKSVERILHDHGILT PSLCFVVPDGYKLTGNVLILLECFVRSSPANFEQKYIEDFKKLEQLKEDLKSVDINLIPLIDGRTSFYNEQIPDWVNDKL ...Details: MEDDMACVKDLVSKYLADNERLSRQKLAFLVQTEPRMLLMEGLKLLSLCIEIDSCNANGCEHNSEDKSVERILHDHGILT PSLCFVVPDGYKLTGNVLILLECFVRSSPANFEQKYIEDFKKLEQLKEDLKSVDINLIPLIDGRTSFYNEQIPDWVNDKL RDTLFSLLRYAQESNSLFEESEYSRLCESLSMTSGRLSGVESLNVLLDNRSSHYEEIIASCHQGINNKLTAHEVKLQIEE EYQVFRNRLRKGEITGQFLKVDKSRLLNDFNNLYVDEVTATKDNIEHLIYQFKRASPILRFLYANIGEGNGEERHHTIKE CQMQYWRSFLNKVKSLRILNTRRKLLLIFDALILLASIHDQTRHKCSKGWLGSCFISVNDRLVSLESTKRDLEKWVGRRQ QSERSNTIQPPDKNQILISMFQKTILKATAALKDVGISVEHYKINMEVICPDSYDLILNFDVSGVVPTISYQRTEDEKFP FIMGGVELLESTDLERLSSLSLALVNSMKTSSTVKLRQNEFGPARYQVVRCKEAYCQEFLLSGAEFQLIYQKTGECSKCY AINDNRVGEICSFYADPKRYFPAIFSAEVLQTTVSTMISWVKDCSELEEQLCNINSLTKMILVLILAHPSKRSQKLLQNL RYFIMAYVSDYHHKDLIDKLREELITDVEFLLYRLVRALVNLILSEDVKSMMTNRFKFILNISYMCHFITKETPDRLTDQ IKCFEKFLEPKLEFGHVSINPADVATEEELDDMVYNAKKFLSKEGCTSIKGPDYKKPGVSKRFLSLLTSSFNNGSLFKES EVKREIKDPLVTSGCATALDLASNKSVVVNKYTDGSRVLNYDFNKLTALAVSQLTEVFSRKGKHLLNKQDYDYKVQQAMS NLVLGPRQNKVGADEADLDEILLDGGASVYFDQLKETVERIIDQYREPVKPGSNPNGGDQPSVNDLDEVVPNKFYIRLIK GELSNHMVEDFDYDVLPGNFYEEFCDAVYKNNKLKERYFYCGQMSQCPIGELTKAVATRTYFDQEYFQCFKSILLIMNAN TLMGRYTHYKSRNLNFKFDMGRLSDDVRISERESNSEALSKALSLTNCTTAMLKNLCFYSQESPQSYSSTGPDTGRLKFS LSYKEQVGGNRELYIGDLRTKMFTRLIEDYFEALSLQLSGSCLNNEREFENAILSMKLNVSLAHVSYSMDHSKWGPMMCP FLFLATLQNLIFLSKDLQADIKGRDYLSTLLTWHMHKMVEIPFNVVSAMMKSFIKAQLGLKKKTTQSITEDFFYSNFQIG VVPSHVSSILDMGQGILHNTSDFYALISERFINYAISCICGGTIDAYTSSDDQISLFDQVLTELMQRDPEEFKTLIEFHY YMSDQLNKFVSPKSVIGRFVAEFKSRFYVWGDEVPLLTKFVAAALHNIKCKEPHQLAETIDTIIDQSVANGVPVHLCNLI QKRTLSLLQYARYPIDPFLLNCETDVRDWVDGNRSYRIMRQIERLIPDACGRIRSMLRKLYNKLKTGQLHEEFTTNYLSS EHLSSLSNLCELLGVEPPSESDLEFSWLNLAAHHPLRMVLRQKIIYSGAVNLDDEKVPTIVKTIQNKLSSTFTRGAQKLL SEAINKSAFQSSIASGFVGLCRTLGSKCVRGPNKESLYIKSIQSLISDIQGIEPLIDSHGVQYWRVPLNIRDGNEGVISY FRPLLWDYMCISLSTAIELGAWVLGEPKKVRVLEFFKHNPCDYFPLKPAASKLLEDRVGLNHIIHSLRRLYPSVFEKHIL PFMSDLASTKMKWSPRIKFLDLCVALDVNCEALSLVSHIVKWKREEHYIVLSSELRLSHTRTHEPMVEERVVSTSDAVDN FMRQIYFESYVRSFVATTRTLGSFTWFPHKTSVPEGEGLQRLGPFSSFVEKAIHKGIERPMFKHDLMMGYAWIDFDIEPA RFNHNQLIASGLVGPRFDSLEDFFDAVESLPPGSAKLSQTVRFRIKSQDASFKESFAIHLDYTGSINQQTKYLVHEVSAM YSGAVSPCVLSDCWRLVLSGPTFKGKSAWYVDTEIVNEFLTDTNQLGHVTPVEIVVDMEKLQFTEYDFVLVGPCVEPVPL VVHRGGLWECDKKLASFTPVVQDQDLEMFVKEVGDSSLDLLIGALSAMILDRLKLRMQWSEVDIVSMLKAAMPSNSVKVL NAVLEAVDDWVDFKGYALCYSKSRKKVMVHSSGGKLRLKGRTCEELVKEDEGIEDIE Source: (gene. exp.) ![]() ![]() References: UniProt: A0A3S8NV63, RNA-directed RNA polymerase, Hydrolases; Acting on ester bonds |
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-RNA chain , 3 types, 4 molecules DREM
#2: RNA chain | Mass: 6452.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
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#3: RNA chain | Mass: 6069.649 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #4: RNA chain | | Mass: 2854.782 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 3 types, 7 molecules ![](data/chem/img/2KH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/ZN.gif)
#5: Chemical | ChemComp-2KH / | ||
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#6: Chemical | ChemComp-MN / #7: Chemical | ChemComp-ZN / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component |
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Molecular weight | Value: 0.253346 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 49.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79600 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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