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- EMDB-12956: Lassa virus L protein in an elongation conformation [ELONGATION] -

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Basic information

Entry
Database: EMDB / ID: EMD-12956
TitleLassa virus L protein in an elongation conformation [ELONGATION]
Map dataLassa virus L protein in an elongation conformation [ELONGATION]
Sample
  • Complex: RNA-directed RNA polymerase L Lassa mammarenavirus
    • Complex: RNA-directed RNA polymerase L
      • Protein or peptide: RNA-directed RNA polymerase L
    • Complex: 5' RNA, 3' RNA
      • RNA: 5' RNA
      • RNA: 3' RNA
    • Complex: product RNA
      • RNA: product RNA
  • Ligand: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
  • Ligand: MANGANESE (II) ION
  • Ligand: ZINC ION
KeywordsLassa virus RNA-dependent RNA polymerase viral RNA / VIRAL PROTEIN
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
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesLassa mammarenavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsKouba T / Vogel D
Funding support Germany, 2 items
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, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ojn
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12956.png

Downloads & links

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Map

FileDownload / File: emd_12956.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLassa virus L protein in an elongation conformation [ELONGATION]
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16 / Movie #1: 0.16
Minimum - Maximum-0.24683507 - 0.7842376
Average (Standard dev.)0.0024532669 (±0.024077961)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z272.000272.000272.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2470.7840.002

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Supplemental data

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Additional map: #1

Fileemd_12956_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_12956_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12956_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA-directed RNA polymerase L Lassa mammarenavirus

EntireName: RNA-directed RNA polymerase L Lassa mammarenavirus
Components
  • Complex: RNA-directed RNA polymerase L Lassa mammarenavirus
    • Complex: RNA-directed RNA polymerase L
      • Protein or peptide: RNA-directed RNA polymerase L
    • Complex: 5' RNA, 3' RNA
      • RNA: 5' RNA
      • RNA: 3' RNA
    • Complex: product RNA
      • RNA: product RNA
  • Ligand: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
  • Ligand: MANGANESE (II) ION
  • Ligand: ZINC ION

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Supramolecule #1: RNA-directed RNA polymerase L Lassa mammarenavirus

SupramoleculeName: RNA-directed RNA polymerase L Lassa mammarenavirus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 253.346 KDa

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Supramolecule #2: RNA-directed RNA polymerase L

SupramoleculeName: RNA-directed RNA polymerase L / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Lassa mammarenavirus

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Supramolecule #3: 5' RNA, 3' RNA

SupramoleculeName: 5' RNA, 3' RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Lassa mammarenavirus

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Supramolecule #4: product RNA

SupramoleculeName: product RNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Lassa mammarenavirus

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Macromolecule #1: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 1
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
Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Lassa mammarenavirus
Molecular weightTheoretical: 253.656938 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEDDMACVKD LVSKYLADNE RLSRQKLAFL VQTEPRMLLM EGLKLLSLCI EIDSCNANGC EHNSEDKSVE RILHDHGILT PSLCFVVPD GYKLTGNVLI LLECFVRSSP ANFEQKYIED FKKLEQLKED LKSVDINLIP LIDGRTSFYN EQIPDWVNDK L RDTLFSLL ...String:
MEDDMACVKD LVSKYLADNE RLSRQKLAFL VQTEPRMLLM EGLKLLSLCI EIDSCNANGC EHNSEDKSVE RILHDHGILT PSLCFVVPD GYKLTGNVLI LLECFVRSSP ANFEQKYIED FKKLEQLKED LKSVDINLIP LIDGRTSFYN EQIPDWVNDK L RDTLFSLL RYAQESNSLF EESEYSRLCE SLSMTSGRLS GVESLNVLLD NRSSHYEEII ASCHQGINNK LTAHEVKLQI EE EYQVFRN RLRKGEITGQ FLKVDKSRLL NDFNNLYVDE VTATKDNIEH LIYQFKRASP ILRFLYANIG EGNGEERHHT IKE CQMQYW RSFLNKVKSL RILNTRRKLL LIFDALILLA SIHDQTRHKC SKGWLGSCFI SVNDRLVSLE STKRDLEKWV GRRQ QSERS NTIQPPDKNQ ILISMFQKTI LKATAALKDV GISVEHYKIN MEVICPDSYD LILNFDVSGV VPTISYQRTE DEKFP FIMG GVELLESTDL ERLSSLSLAL VNSMKTSSTV KLRQNEFGPA RYQVVRCKEA YCQEFLLSGA EFQLIYQKTG ECSKCY AIN DNRVGEICSF YADPKRYFPA IFSAEVLQTT VSTMISWVKD CSELEEQLCN INSLTKMILV LILAHPSKRS QKLLQNL RY FIMAYVSDYH HKDLIDKLRE ELITDVEFLL YRLVRALVNL ILSEDVKSMM TNRFKFILNI SYMCHFITKE TPDRLTDQ I KCFEKFLEPK LEFGHVSINP ADVATEEELD DMVYNAKKFL SKEGCTSIKG PDYKKPGVSK RFLSLLTSSF NNGSLFKES EVKREIKDPL VTSGCATALD LASNKSVVVN KYTDGSRVLN YDFNKLTALA VSQLTEVFSR KGKHLLNKQD YDYKVQQAMS NLVLGPRQN KVGADEADLD EILLDGGASV YFDQLKETVE RIIDQYREPV KPGSNPNGGD QPSVNDLDEV VPNKFYIRLI K GELSNHMV EDFDYDVLPG NFYEEFCDAV YKNNKLKERY FYCGQMSQCP IGELTKAVAT RTYFDQEYFQ CFKSILLIMN AN TLMGRYT HYKSRNLNFK FDMGRLSDDV RISERESNSE ALSKALSLTN CTTAMLKNLC FYSQESPQSY SSTGPDTGRL KFS LSYKEQ VGGNRELYIG DLRTKMFTRL IEDYFEALSL QLSGSCLNNE REFENAILSM KLNVSLAHVS YSMDHSKWGP MMCP FLFLA TLQNLIFLSK DLQADIKGRD YLSTLLTWHM HKMVEIPFNV VSAMMKSFIK AQLGLKKKTT QSITEDFFYS NFQIG VVPS HVSSILDMGQ GILHNTSDFY ALISERFINY AISCICGGTI DAYTSSDDQI SLFDQVLTEL MQRDPEEFKT LIEFHY YMS DQLNKFVSPK SVIGRFVAEF KSRFYVWGDE VPLLTKFVAA ALHNIKCKEP HQLAETIDTI IDQSVANGVP VHLCNLI QK RTLSLLQYAR YPIDPFLLNC ETDVRDWVDG NRSYRIMRQI ERLIPDACGR IRSMLRKLYN KLKTGQLHEE FTTNYLSS E HLSSLSNLCE LLGVEPPSES DLEFSWLNLA AHHPLRMVLR QKIIYSGAVN LDDEKVPTIV KTIQNKLSST FTRGAQKLL SEAINKSAFQ SSIASGFVGL CRTLGSKCVR GPNKESLYIK SIQSLISDIQ GIEPLIDSHG VQYWRVPLNI RDGNEGVISY FRPLLWDYM CISLSTAIEL GAWVLGEPKK VRVLEFFKHN PCDYFPLKPA ASKLLEDRVG LNHIIHSLRR LYPSVFEKHI L PFMSDLAS TKMKWSPRIK FLDLCVALDV NCEALSLVSH IVKWKREEHY IVLSSELRLS HTRTHEPMVE ERVVSTSDAV DN FMRQIYF ESYVRSFVAT TRTLGSFTWF PHKTSVPEGE GLQRLGPFSS FVEKAIHKGI ERPMFKHDLM MGYAWIDFDI EPA RFNHNQ LIASGLVGPR FDSLEDFFDA VESLPPGSAK LSQTVRFRIK SQDASFKESF AIHLDYTGSI NQQTKYLVHE VSAM YSGAV SPCVLSDCWR LVLSGPTFKG KSAWYVDTEI VNEFLTDTNQ LGHVTPVEIV VDMEKLQFTE YDFVLVGPCV EPVPL VVHR GGLWECDKKL ASFTPVVQDQ DLEMFVKEVG DSSLDLLIGA LSAMILDRLK LRMQWSEVDI VSMLKAAMPS NSVKVL NAV LEAVDDWVDF KGYALCYSKS RKKVMVHSSG GKLRLKGRTC EELVKEDEGI EDIE

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: 5' RNA

MacromoleculeName: 5' RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Lassa mammarenavirus
Molecular weightTheoretical: 6.452911 KDa
SequenceString:
GCGCACCGGG GAUCCUAGGC

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Macromolecule #3: 3' RNA

MacromoleculeName: 3' RNA / type: rna / ID: 3 / Number of copies: 2
Source (natural)Organism: Lassa mammarenavirus
Molecular weightTheoretical: 6.069649 KDa
SequenceString:
GCCUAGGAUC CACUGUGCG

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Macromolecule #4: product RNA

MacromoleculeName: product RNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Lassa mammarenavirus
Molecular weightTheoretical: 2.854782 KDa
SequenceString:
UACGCACAG

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Macromolecule #5: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phos...

MacromoleculeName: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
type: ligand / ID: 5 / Number of copies: 1 / Formula: 2KH
Molecular weightTheoretical: 483.156 Da
Chemical component information

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

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Macromolecule #6: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 6 / Number of copies: 5 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79600
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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