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- PDB-7ojn: Lassa virus L protein in an elongation conformation [ELONGATION] -

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Basic information

Entry
Database: PDB / ID: 7ojn
TitleLassa virus L protein in an elongation conformation [ELONGATION]
Components
  • 3' RNA
  • 5' RNA
  • RNA-directed RNA polymerase L
  • product RNA
KeywordsVIRAL PROTEIN / Lassa virus RNA-dependent RNA polymerase viral RNA
Function / homology
Function and homology information


negative stranded viral RNA replication / cap snatching / virion component / host cell / Hydrolases; Acting on ester bonds / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / metal ion binding
Similarity search - Function
RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / : / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
Chem-2KH / : / RNA / RNA (> 10) / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesLassa mammarenavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsKouba, T. / Vogel, D. / Thorkelsson, S. / Quemin, E. / Williams, H.M. / Milewski, M. / Busch, C. / Gunther, S. / Grunewald, K. / Rosenthal, M. / Cusack, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
Leibniz AssociationK27/2017 Germany
German Research Foundation (DFG)INST 152/777-1 FUGG Germany
CitationJournal: Nat Commun / Year: 2021
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
DepositionMay 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
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Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
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Revision 1.2May 1, 2024Group: Data collection / Structure summary / Category: audit_author / chem_comp_atom / chem_comp_bond / Item: _audit_author.name
Revision 1.3Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
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Structure visualization

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Assembly

Deposited unit
L: RNA-directed RNA polymerase L
D: 5' RNA
R: 3' RNA
M: product RNA
E: 3' RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,92712
Polymers275,1045
Non-polymers8237
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 1 molecules L

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


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.) Lassa mammarenavirus / Production host: Trichoplusia ni (cabbage looper)
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 5' RNA


Mass: 6452.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lassa mammarenavirus
#3: RNA chain 3' RNA


Mass: 6069.649 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Lassa mammarenavirus
#4: RNA chain product RNA


Mass: 2854.782 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lassa mammarenavirus

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Non-polymers , 3 types, 7 molecules

#5: Chemical ChemComp-2KH / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1RNA-directed RNA polymerase L Lassa mammarenavirusCOMPLEX#1-#40MULTIPLE SOURCES
2RNA-directed RNA polymerase LCOMPLEX#11RECOMBINANT
35' RNA, 3' RNACOMPLEX#2-#31RECOMBINANT
4product RNACOMPLEX#41NATURAL
Molecular weightValue: 0.253346 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Lassa mammarenavirus11620
33Lassa mammarenavirus11620
44Lassa mammarenavirus11620
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Trichoplusia ni (cabbage looper)7111
33synthetic construct (others)32630
Buffer solutionpH: 7
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 49.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79600 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217392
ELECTRON MICROSCOPYf_angle_d0.3923672
ELECTRON MICROSCOPYf_dihedral_angle_d9.3456613
ELECTRON MICROSCOPYf_chiral_restr0.0362707
ELECTRON MICROSCOPYf_plane_restr0.0032855

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