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- EMDB-51402: Structure of Nipah Virus RNA Polymerase Complex - Apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-51402
TitleStructure of Nipah Virus RNA Polymerase Complex - Apo state
Map data
Sample
  • Complex: Nipah Virus RdRp Complex in Apo state.
    • Protein or peptide: Phosphoprotein
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION
KeywordsRNA Polymerase / Nipah Virus / negative strand RNA Virus / VIRAL PROTEIN
Function / homology
Function and homology information


negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / molecular adaptor activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / symbiont-mediated suppression of host innate immune response ...negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / molecular adaptor activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / ATP binding
Similarity search - Function
Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Mononegavirales RNA-directed RNA polymerase catalytic domain ...Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase
Similarity search - Domain/homology
RNA-directed RNA polymerase L / Phosphoprotein
Similarity search - Component
Biological speciesHenipavirus nipahense
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsSala F / Ditter K / Dybkov O / Urlaub H / Hillen HS
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1565 Germany
German Research Foundation (DFG)SFB1190 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of Nipah virus RNA synthesis.
Authors: Fernanda A Sala / Katja Ditter / Olexandr Dybkov / Henning Urlaub / Hauke S Hillen /
Abstract: Nipah virus (NiV) is a non-segmented negative-strand RNA virus (nsNSV) with high pandemic potential, as it frequently causes zoonotic outbreaks and can be transmitted from human to human. Its RNA- ...Nipah virus (NiV) is a non-segmented negative-strand RNA virus (nsNSV) with high pandemic potential, as it frequently causes zoonotic outbreaks and can be transmitted from human to human. Its RNA-dependent RNA polymerase (RdRp) complex, consisting of the L and P proteins, carries out viral genome replication and transcription and is therefore an attractive drug target. Here, we report cryo-EM structures of the NiV polymerase complex in the apo and in an early elongation state with RNA and incoming substrate bound. The structure of the apo enzyme reveals the architecture of the NiV L-P complex, which shows a high degree of similarity to other nsNSV polymerase complexes. The structure of the RNA-bound NiV L-P complex shows how the enzyme interacts with template and product RNA during early RNA synthesis and how nucleoside triphosphates are bound in the active site. Comparisons show that RNA binding leads to rearrangements of key elements in the RdRp core and to ordering of the flexible C-terminal domains of NiV L required for RNA capping. Taken together, these results reveal the first structural snapshots of an actively elongating nsNSV L-P complex and provide insights into the mechanisms of genome replication and transcription by NiV and related viruses.
History
DepositionAug 22, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51402.png

Downloads & links

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Map

FileDownload / File: emd_51402.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 400.32 Å		0.83 Å/pix.
x 480 pix.
= 400.32 Å		0.83 Å/pix.
x 480 pix.
= 400.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0179
Minimum - Maximum-0.094230145 - 0.18395808
Average (Standard dev.)0.0000027559208 (±0.0021736769)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 400.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51402_msk_1.map
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Additional map: Post-processed map.

Fileemd_51402_additional_1.map
AnnotationPost-processed map.
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Additional map: Unsharpened map.

Fileemd_51402_additional_2.map
AnnotationUnsharpened map.
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Half map: Half-map 1.

Fileemd_51402_half_map_1.map
AnnotationHalf-map 1.
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Half map: Half-map 2.

Fileemd_51402_half_map_2.map
AnnotationHalf-map 2.
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Sample components

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Entire : Nipah Virus RdRp Complex in Apo state.

EntireName: Nipah Virus RdRp Complex in Apo state.
Components
  • Complex: Nipah Virus RdRp Complex in Apo state.
    • Protein or peptide: Phosphoprotein
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION

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Supramolecule #1: Nipah Virus RdRp Complex in Apo state.

SupramoleculeName: Nipah Virus RdRp Complex in Apo state. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 570 KDa

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Macromolecule #1: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 78.39032 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDKLELVNDG LNIIDFIQKN QKEIQKTYGR SSIQQPSIKD QTKAWEDFLQ CTSGESEQVE GGMSKDDGDV ERRNLEDLSS TSPTDGTIG KRVSNTRDWA EGSDDIQLDP VVTDVVYHDH GGECTGYGFT SSPERGWSDY TSGANNGNVC LVSDAKMLSY A PEIAVSKE ...String:
MDKLELVNDG LNIIDFIQKN QKEIQKTYGR SSIQQPSIKD QTKAWEDFLQ CTSGESEQVE GGMSKDDGDV ERRNLEDLSS TSPTDGTIG KRVSNTRDWA EGSDDIQLDP VVTDVVYHDH GGECTGYGFT SSPERGWSDY TSGANNGNVC LVSDAKMLSY A PEIAVSKE DRETDLVHLE NKLSTTGLNP TAVPFTLRNL SDPAKDSPVI AEHYYGLGVK EQNVGPQTSR NVNLDSIKLY TS DDEEADQ LEFEDEFAGS SSEVIVGISP EDEEPSSVGG KPNESIGRTI EGQSIRDNLQ AKDNKSTDVP GAGPKDSAVK EEP PQKRLP MLAEEFECSG SEDPIIRELL KENSLINCQQ GKDAQPPYHW SIERSISPDK TEIVNGAVQT ADRQRPGTPM PKSR GIPIK KGTDAKYPSA GTENVPGSKS GATRHVRGSP PYQEGKSVNA ENVQLNASTA VKETDKSEVN PVDDNDSLDD KYIMP SDDF SNTFFPHDTD RLNYHADHLG DYDLETLCEE SVLMGVINSI KLINLDMRLN HIEEQVKEIP KIINKLESID RVLAKT NTA LSTIEGHLVS MMIMIPGKGK GERKGKNNPE LKPVIGRDIL EQQSLFSFDN VKNFRDGSLT NEPYGAAVQL REDLILP EL NFEETNASQF VPMADDSSRD VIKTLIRTHI KDRELRSELI GYLNKAENDE EIQEIANTVN DIIDGNI

UniProtKB: Phosphoprotein

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Macromolecule #2: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 257.706219 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAADELSIS DIIYPECHLD SPIVSGKLIS AIEYAQLRHN QPSDDKRLSE NIRLNLHGKR KSLYILRQSK QGDYIRNNIK NLKEFMHIA YPECNNILFS ITSQGMTSKL DNIMKKSFKA YNIISKKVIG MLQNITRNLI TQDRRDEIIN IHECRRLGDL G KNMSQSKW ...String:
SNAADELSIS DIIYPECHLD SPIVSGKLIS AIEYAQLRHN QPSDDKRLSE NIRLNLHGKR KSLYILRQSK QGDYIRNNIK NLKEFMHIA YPECNNILFS ITSQGMTSKL DNIMKKSFKA YNIISKKVIG MLQNITRNLI TQDRRDEIIN IHECRRLGDL G KNMSQSKW YECFLFWFTI KTEMRAVIKN SQKPKFRSDS CIIHMRDKST EIILNPNLIC IFKSDKTGKK CYYLTPEMVL MY CDVLEGR MMMETTVKSD IKYQPLISRS NALWGLIDPL FPVMGNRIYN IVSMIEPLVL ALLQLKDEAR ILRGAFLHHC IKE MHQELS ECGFTDQKIR SMFIDDLLSI LNIDNIHLLA EFFSFFRTFG HPILEAKVAA EKVREHMLAD KVLEYAPIMK AHAI FCGTI INGYRDRHGG AWPPLYLPAH ASKHIIRLKN SGESLTIDDC VKNWESFCGI QFDCFMELKL DSDLSMYMKD KALSP IKDE WDSVYPREVL SYTPPKSTEP RRLVDVFVND ENFDPYNMLE YVLSGAYLED EQFNVSYSLK EKETKQAGRL FAKMTY KMR ACQVIAEALI ASGVGKYFKE NGMVKDEHEL LKTLFQLSIS SVPRGNSQGN DPQSINNIER DFQYFKGVTT NVKDKKN NS FNKVKSALNN PCQADGVHHN MSPNTRNRYK CSNTSKSFLD YHTEFNPHNH YKSDNTEAAV LSRYEDNTGT KFDTVSAF L TTDLKKFCLN WRYESMAIFA ERLDEIYGLP GFFNWMHKRL ERSVIYVADP NCPPNIDKHM ELEKTPEDDI FIHYPKGGI EGYSQKTWTI ATIPFLFLSA YETNTRIAAI VQGDNESIAI TQKVHPNLPY KVKKEICAKQ AQLYFERLRM NLRALGHNLK ATETIISTH LFIYSKKIHY DGAVLSQALK SMSRCCFWSE TLVDETRSAC SNISTTIAKA IENGLSRNVG YCINILKVIQ Q LLISTEFS INETLTLDVT SPISNNLDWL ITAALIPAPI GGFNYLNLSR IFVRNIGDPV TASLADLKRM IDHSIMTESV LQ KVMNQEP GDASFLDWAS DPYSGNLPDS QSITKTIKNI TARTILRNSP NPMLKGLFHD KSFDEDLELA SFLMDRRVIL PRA AHEILD NSLTGAREEI AGLLDTTKGL IRSGLRKSGL QPKLVSRLSH HDYNQFLILN KLLSNRRQND LISSNTCSVD LARA LRSHM WRELALGRVI YGLEVPDALE AMVGRYITGS LECQICEQGN TMYGWFFVPR DSQLDQVDRE HSSIRVPYVG SSTDE RSDI KLGNVKRPTK ALRSAIRIAT VYTWAYGDNE ECWYEAWYLA SQRVNIDLDV LKAITPVSTS NNLSHRLRDK STQFKF AGS VLNRVSRYVN ISNDNLDFRI EGEKVDTNLI YQQAMLLGLS VLEGKFRLRL ETDDYNGIYH LHVKDNCCVK EVADVGQ VD AELPIPEYTE VDNNHLIYDP DPVSEIDCSR LSNQESKSRE LDFPLWSTEE LHDVLAKTVA QTVLEIITKA DKDVLKQH L AIDSDDNINS LITEFLIVDP ELFALYLGQS ISIKWAFEIH HRRPRGRHTM VDLLSDLVSN TSKHTYKVLS NALSHPRVF KRFVNCGLLL PTQGPYLHQQ DFEKLSQNLL VTSYMIYLMN WCDFKKSPFL IAEQDETVIS LREDIITSKH LCVIIDLYAN HHKPPWIID LNPQEKICVL RDFISKSRHV DTSSRSWNTS DLDFVIFYAS LTYLRRGIIK QLRIRQVTEV IDTTTMLRDN I IVENPPIK TGVLDIRGCI IYNLEEILSM NTKSASKKIF NLNSRPSVEN HKYRRIGLNS SSCYKALNLS PLIQRYLPSG AQ RLFIGEG SGSMMLLYQS TLGQSISFYN SGIDGDYIPG QRELKLFPSE YSIAEEDPSL TGKLKGLVVP LFNGRPETTW IGN LDSYEY IINRTAGRSI GLVHSDMESG IDKNVEEILV EHSHLISIAI NVMMEDGLLV SKIAYTPGFP ISRLFNMYRS YFGL VLVCF PVYSNPDSTE VYLLCLQKTV KTIVPPQKVL EHSNLHDEVN DQGITSVIFK IKNSQSKQFH DDLKKYYQID QPFFV PTKI TSDEQVLLQA GLKLNGPEIL KSEISYDIGS DINTLRDTII IMLNEAMNYF DDNRSPSHHL EPYPVLERTR IKTIMN CVT KKVIVYSLIK FKDTKSSELY HIKNNIRRKV LILDFRSKLM TKTLPKGMQE RREKNGFKEV WIVDLSNREV KIWWKII GY ISII

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / 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: 8
Details: 50 mM HEPES pH 8.0, 400 mM NaCl, 6 mM MgCl2, 10% glycerol, 5 mM DTT, 0.01% Tween 20
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.48 sec. / Average electron dose: 48.94 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9886170
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 591312
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 600000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9gjt:
Structure of Nipah Virus RNA Polymerase Complex - Apo state

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