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- EMDB-53349: Apo form of the L protein from Rift Valley Fever Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-53349
TitleApo form of the L protein from Rift Valley Fever Virus
Map data
Sample
  • Complex: Rift Valley Fever Virus L-protein (LPapo)
    • Protein or peptide: RNA-directed RNA polymerase L
KeywordsRift Valley Fever Virus / RNA dependent RNA polymerase / L-protein / Replication / Transcription / VIRAL PROTEIN
Function / homology
Function and homology information


nucleoside binding / host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase, phlebovirus / RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / 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 speciesRift valley fever virus (STRAIN ZH-548 M12)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKral M / Das AR / Kotacka T / Blahosova A / Hodek J / Konvalinka J / Demo G / Kozisek M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: ACS Infect Dis / Year: 2025
Title: Targeting the Rift Valley Fever Virus Polymerase: Resistance Mechanisms and Structural Insights.
Authors: Michal Král' / Amiyaranjan Das / Tomáš Kotačka / Anna Blahošová / Veronika Liščáková / Jan Hodek / Jan Konvalinka / Gabriel Demo / Milan Kožíšek /
Abstract: Rift Valley fever virus (RVFV) is an arbovirus from the family that can cause severe disease in humans and livestock, with outbreaks resulting in substantial economic losses. Despite the ...Rift Valley fever virus (RVFV) is an arbovirus from the family that can cause severe disease in humans and livestock, with outbreaks resulting in substantial economic losses. Despite the availability of attenuated vaccines for animals, there is no approved preventive or therapeutic agent for human RVFV infections. Moreover, the safety and efficacy of the current veterinary vaccines remain uncertain. The RVFV L protein, a 250 kDa polymerase, plays a key role in viral replication and transcription, containing endonuclease, RNA-dependent RNA polymerase (RdRp), and cap-binding domains. Structurally conserved across related viruses and functionally analogous to the influenza virus polymerase, the L protein is a compelling antiviral target. In our study, we screened a library of polymerase inhibitors and identified several compounds with inhibitory activity against the RVFV polymerase. We validated their effect using both live virus assays and a minigenome luciferase reporter system. Resistance mutants were generated, and key mutations conferring resistance to the inhibitors were identified and characterized. Some of these key mutations were structurally analyzed via cryo-electron microscopy, using a new structure of the apo form of wild-type RVFV L protein resolved at 3.5 Å. This structure provides critical insights into how the mutations can influence inhibitor binding and RVFV polymerase function. These findings provide insight into how these mutations may confer resistance by affecting inhibitor binding and polymerase activity.
History
DepositionApr 8, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53349.png

Downloads & links

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Map

FileDownload / File: emd_53349.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 213.504 Å		0.83 Å/pix.
x 256 pix.
= 213.504 Å		0.83 Å/pix.
x 256 pix.
= 213.504 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.25125945 - 0.63323224
Average (Standard dev.)0.0022474816 (±0.03075206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 213.504 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53349_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53349_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Rift Valley Fever Virus L-protein (LPapo)

EntireName: Rift Valley Fever Virus L-protein (LPapo)
Components
  • Complex: Rift Valley Fever Virus L-protein (LPapo)
    • Protein or peptide: RNA-directed RNA polymerase L

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Supramolecule #1: Rift Valley Fever Virus L-protein (LPapo)

SupramoleculeName: Rift Valley Fever Virus L-protein (LPapo) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rift valley fever virus (STRAIN ZH-548 M12)
Molecular weightTheoretical: 243 KDa

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Macromolecule #1: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Rift valley fever virus (STRAIN ZH-548 M12) / Strain: ZH-548
Molecular weightTheoretical: 241.322812 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MDSILSKQLV DKTGFVRVPI KHFDCTMLTL ALPTFDVSKM VDRITIDFNL DDIQGASEIG STLLPSMSID VEDMANFVHD FTFGHLADK TDRLLMREFP MMNAGFDHLS PDMIIKTTSG MYNIVEFTTF RGDERGAFQA AMTKLAKYEV PCENRSQGRT V VLYVVSAY ...String:
MDSILSKQLV DKTGFVRVPI KHFDCTMLTL ALPTFDVSKM VDRITIDFNL DDIQGASEIG STLLPSMSID VEDMANFVHD FTFGHLADK TDRLLMREFP MMNAGFDHLS PDMIIKTTSG MYNIVEFTTF RGDERGAFQA AMTKLAKYEV PCENRSQGRT V VLYVVSAY RHGVWSNLEL EDSEAEEMVY RYRLALSVMD ELRTLFPELS STDEELGKTE RELLAMVSSI QINWSVTESV FP PFSREMF DRFRSSPPDS EYITRIVSRC LINSQEKLIN SSFFAEGNDK ALRFSKNAEE CSLAVERALN QYRAEDNLRD LND HKSTIQ LPPWLSYHDV DGKDLCPLQG LDVRGDHPMC NLWREVVTSA NLEEIERMHD DAAAELEFAL SGVKDRPDER NRYH RVHLN MGSDDSVYIA ALGVNGKKHK ADTLVQQMRD RSKQPFSPDH DVDHISEFLS ACSSDLWATD EDLYSPLSCD KELRL AAQR IHQPSLSERG FNEIITEHYK FMGSRIGSWC QMVSLIGAEL SASVKQHVKP NYFVIKRLLG SGIFLLIKPT SSKSHI FVS FAIKRSCWAF DLSTSRVFKP YIDAGDLLVT DFVSYKLSKL TNLCKCVSLM ESSFSFWAEA FGIPSWNFVG DLFRSSD SA AMDASYMGKL SLLTLLEDKA ATEELQTIAR YIIMEGFVSP PEIPKPHKMT SKFPKVLRSE LQVYLLNCLC RTIQRIAG E PFILKKKDGS ISWGGMFNPF SGRPLLDMQP LISCCYNGYF KNKEEETEPS SLSGMYKKII ELEHLRPQSD AFLGYKDPE LPRMHEFSVS YLKEACNHAK LVLRSLYGQN FMEQIDNQII RELSGLTLER LATLKATSNF NENWYVYKDV ADKNYTRDKL LVKMSKYAS EGKSLAIQKF EDCMRQIESQ GCMHICLFKK QQHGGLREIY VMGAEERIVQ SVVETIARSI GKFFASDTLC N PPNKVKIP ETHGIRARKQ CKGPVWTCAT SDDARKWNQG HFVTKFALML CEFTSPKWWP LIIRGCSMFT RKRMMMNLNY LK ILDGHRE LDIRDDFVMD LFKAYHGEAE VPWAFKGKTY LETTTGMMQG ILHYTSSLLH TIHQEYIRSL SFKIFNLKVA PEM SKSLVC DMMQGSDDSS MLISFPADDE KVLTRCKVAA AICFRMKKEL GVYLAIYPSE KSTANTDFVM EYNSEFYFHT QHVR PTIRW IAACCSLPEV ETLVARQEEA SNLMTSVTEG GGSFSLAAMI QQAQCTLHYM LMGMGVSELF LEYKKAVLKW NDPGL GFFL LDNPYACGLG GFRFNLFKAI TRTDLQKLYA FFMKKVKGSA ARDWADEDVT IPETCSVSPG GALILSSSLK WGSRKK FQK LRDRLNIPEN WIELINENPE VLYRAPRTGP EILLRIAEKV HSPGVVSSLS SGNAVCKVMA SAVYFLSATI FEDTGRP EF NFLEDSKYSL LQKMAAYSGF HGFNDMEPED ILFLFPNIEE LESLDSIVYN KGEIDIIPRV NIRDATQTRV TIFNEQKT L RTSPEKLVSD KWFGTQKSRI GKTTFLAEWE KLKKIVKWLE DTPEATLAHT PLNNHIQVRN FFARMESKPR TVRITGAPV KKRSGVSKIA MVIRDNFSRM GHLRGVEDLA GFTRSVSAEI LKHFLFCILQ GPYSESYKLQ LIYRVLSSVS NVEIKESDGK TKTNLIGIL QRFLDGDHVV PIIEEMGAGT VGGFIKRQQS KVVQNKVVYY GVGIWRGFMD GYQVHLEIEN DIGQPPRLRN V TTNCQSSP WDLSIPIRQW AEDMGVTNNQ DYSSKSSRGA RYWMHSFRMQ GPSKPFGCPV YIIKGDMSDV IRLRKEEVEM KV RGSTLNL YTKHHSHQDL HILSYTASDN DLSPGIFKSI SDEGVAQALQ LFEREPSNCW VRCESVAPKF ISAILEICEG KRQ IKGINR TRLSEIVRIC SESSLRSKVG SMFSFVANVE EAHDVDYDAL MDLMIEDAKN NAFSHVVDCI ELDVSGPYEM ESFD TSDVN LFGPAHYKDI SSLSMIAHPL MDKFVDYAIS KMGRASVRKV LETGRCSSKD YDLSKVLFRT LQRPEESIRI DDLEL YEET DVADDMLGGS AWSHPQFEKG GGSGGGSGGS AWSHPQFEK

UniProtKB: RNA-directed RNA polymerase L

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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

Concentration0.48 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMTris-HClTris-hydrochloride
250.0 mMNaClSodium Chloride
2.0 mMDTTDithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
Details: the grid was glow discharged for 45 seconds at 40W power and 5W range using a Gatan Solaris II
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9046 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 105000
Sample stageSpecimen 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

Particle selectionNumber selected: 2403715
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185424
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 74978

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Atomic model buiding 1

Initial model
PDB IDChain

7eei

chain_id: A, source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qtb:
Apo form of the L protein from Rift Valley Fever Virus

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