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- EMDB-68072: Cryo-EM Structure of Nipah Virus Polymerase in complex with G671 -

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Entry
Database: EMDB / ID: EMD-68072
TitleCryo-EM Structure of Nipah Virus Polymerase in complex with G671
Map data
Sample
  • Complex: Cryo-EM Structure of Nipah Virus Polymerase in complex with G671
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ~{N}-[4-[(2~{S})-2-[2-[4-[2-(3-cyanophenyl)ethanoyl]piperazin-1-yl]ethyl]piperidin-1-yl]sulfonylphenyl]-2-methyl-5-(trifluoromethyl)pyrazole-3-carboxamide
  • Ligand: ZINC ION
KeywordsPolymerase / inhibitor / nipah virus / complex / REPLICATION / VIRAL PROTEIN
Function / homology
Function and homology information


negative stranded viral RNA transcription / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / molecular adaptor activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase ...negative stranded viral RNA transcription / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / molecular adaptor activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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 / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Mononegavirus L protein 2-O-ribose methyltransferase ...Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic 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: 2.92 Å
AuthorsXue L / Gui J / Chang T / Pan H / Xiong X
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32400116 to L.X China
National Natural Science Foundation of China (NSFC)82341085 to X.X China
CitationJournal: Cell / Year: 2026
Title: Differential inhibition of Morbillivirus and Henipavirus polymerases by ERDRP-0519 and structure-guided inhibitor optimization.
Authors: Lu Xue / Jiacheng Gui / Shenghua Gao / Xiaoxiao Gao / Tiancai Chang / Hainei Pan / Jielin Tang / Mingxia Zhang / Zimu Li / Binqian Zou / Heyu Zhao / Longyu Wang / Mei Li / Lijun Rong / ...Authors: Lu Xue / Jiacheng Gui / Shenghua Gao / Xiaoxiao Gao / Tiancai Chang / Hainei Pan / Jielin Tang / Mingxia Zhang / Zimu Li / Binqian Zou / Heyu Zhao / Longyu Wang / Mei Li / Lijun Rong / Richard K Plemper / Xinwen Chen / Jun He / Rongjuan Pei / Peng Zhan / Xiaoli Xiong /
Abstract: ERDRP-0519 is a non-nucleoside polymerase inhibitor developed against measles virus (MeV) of the Morbillivirus genus. Here, we show that ERDRP-0519 also cross-inhibits Nipah virus (NiV) of the ...ERDRP-0519 is a non-nucleoside polymerase inhibitor developed against measles virus (MeV) of the Morbillivirus genus. Here, we show that ERDRP-0519 also cross-inhibits Nipah virus (NiV) of the Henipavirus genus with reduced potency. ERDRP-0519 binds to a shared pocket within the RNA-dependent RNA polymerase (RdRp) palm domains of MeV, peste des petits ruminants virus (PPRV), and NiV polymerases. ERDRP-0519 forms more extensive interactions with Morbillivirus polymerases, whereas binding to NiV polymerase requires substantial RdRp motif rearrangements, likely incurring an energetic cost and resulting in reduced affinity. ERDRP-0519 binding impedes RNA synthesis by sterically blocking RNA and nucleotide binding. Guided by these insights, we designed GL22 and G671, ERDRP-0519 derivatives with extended moieties that engage additional cross-domain RdRp contacts in the NiV polymerase. These derivatives exert more extensive steric hindrance to RNA and nucleotide binding, enhancing biochemical inhibition potency. These findings elucidate the molecular mechanism of ERDRP-0519 action and guide structure-based inhibitor design.
History
DepositionJan 3, 2026-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68072.png

Downloads & links

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Map

FileDownload / File: emd_68072.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 300 pix.
= 262.8 Å		0.88 Å/pix.
x 300 pix.
= 262.8 Å		0.88 Å/pix.
x 300 pix.
= 262.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.876 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.45571402 - 0.78944546
Average (Standard dev.)0.0000075502844 (±0.02149422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 262.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_68072_msk_1.map
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Half map: #2

Fileemd_68072_half_map_1.map
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Half map: #1

Fileemd_68072_half_map_2.map
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Sample components

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Entire : Cryo-EM Structure of Nipah Virus Polymerase in complex with G671

EntireName: Cryo-EM Structure of Nipah Virus Polymerase in complex with G671
Components
  • Complex: Cryo-EM Structure of Nipah Virus Polymerase in complex with G671
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ~{N}-[4-[(2~{S})-2-[2-[4-[2-(3-cyanophenyl)ethanoyl]piperazin-1-yl]ethyl]piperidin-1-yl]sulfonylphenyl]-2-methyl-5-(trifluoromethyl)pyrazole-3-carboxamide
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM Structure of Nipah Virus Polymerase in complex with G671

SupramoleculeName: Cryo-EM Structure of Nipah Virus Polymerase in complex with G671
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Henipavirus nipahense

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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: Henipavirus nipahense
Molecular weightTheoretical: 257.565156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADELSISDI IYPECHLDSP IVSGKLISAI EYAQLRHNQP SDDKRLSENI RLNLHGKRKS LYILRQSKQG DYIRNNIKNL KEFMHIAYP ECNNILFSIT SQGMTSKLDN IMKKSFKAYN IISKKVIGML QNITRNLITQ DRRDEIINIH ECRRLGDLGK N MSQSKWYE ...String:
MADELSISDI IYPECHLDSP IVSGKLISAI EYAQLRHNQP SDDKRLSENI RLNLHGKRKS LYILRQSKQG DYIRNNIKNL KEFMHIAYP ECNNILFSIT SQGMTSKLDN IMKKSFKAYN IISKKVIGML QNITRNLITQ DRRDEIINIH ECRRLGDLGK N MSQSKWYE CFLFWFTIKT EMRAVIKNSQ KPKFRSDSCI IHMRDKSTEI ILNPNLICIF KSDKTGKKCY YLTPEMVLMY CD VLEGRMM METTVKSDIK YQPLISRSNA LWGLIDPLFP VMGNRIYNIV SMIEPLVLAL LQLKDEARIL RGAFLHHCIK EMH QELSEC GFTDQKIRSM FIDDLLSILN IDNIHLLAEF FSFFRTFGHP ILEAKVAAEK VREHMLADKV LEYAPIMKAH AIFC GTIIN GYRDRHGGAW PPLYLPAHAS KHIIRLKNSG ESLTIDDCVK NWESFCGIQF DCFMELKLDS DLSMYMKDKA LSPIK DEWD SVYPREVLSY TPPKSTEPRR LVDVFVNDEN FDPYNMLEYV LSGAYLEDEQ FNVSYSLKEK ETKQAGRLFA KMTYKM RAC QVIAEALIAS GVGKYFKENG MVKDEHELLK TLFQLSISSV PRGNSQGNDP QSINNIERDF QYFKGVTTNV KDKKNNS FN KVKSALNNPC QADGVHHNMS PNTRNRYKCS NTSKSFLDYH TEFNPHNHYK SDNTEAAVLS RYEDNTGTKF DTVSAFLT T DLKKFCLNWR YESMAIFAER LDEIYGLPGF FNWMHKRLER SVIYVADPNC PPNIDKHMEL EKTPEDDIFI HYPKGGIEG YSQKTWTIAT IPFLFLSAYE TNTRIAAIVQ GDNESIAITQ KVHPNLPYKV KKEICAKQAQ LYFERLRMNL RALGHNLKAT ETIISTHLF IYSKKIHYDG AVLSQALKSM SRCCFWSETL VDETRSACSN ISTTIAKAIE NGLSRNVGYC INILKVIQQL L ISTEFSIN ETLTLDVTSP ISNNLDWLIT AALIPAPIGG FNYLNLSRIF VRNIGDPVTA SLADLKRMID HSIMTESVLQ KV MNQEPGD ASFLDWASDP YSGNLPDSQS ITKTIKNITA RTILRNSPNP MLKGLFHDKS FDEDLELASF LMDRRVILPR AAH EILDNS LTGAREEIAG LLDTTKGLIR SGLRKSGLQP KLVSRLSHHD YNQFLILNKL LSNRRQNDLI SSNTCSVDLA RALR SHMWR ELALGRVIYG LEVPDALEAM VGRYITGSLE CQICEQGNTM YGWFFVPRDS QLDQVDREHS SIRVPYVGSS TDERS DIKL GNVKRPTKAL RSAIRIATVY TWAYGDNEEC WYEAWYLASQ RVNIDLDVLK AITPVSTSNN LSHRLRDKST QFKFAG SVL NRVSRYVNIS NDNLDFRIEG EKVDTNLIYQ QAMLLGLSVL EGKFRLRLET DDYNGIYHLH VKDNCCVKEV ADVGQVD AE LPIPEYTEVD NNHLIYDPDP VSEIDCSRLS NQESKSRELD FPLWSTEELH DVLAKTVAQT VLEIITKADK DVLKQHLA I DSDDNINSLI TEFLIVDPEL FALYLGQSIS IKWAFEIHHR RPRGRHTMVD LLSDLVSNTS KHTYKVLSNA LSHPRVFKR FVNCGLLLPT QGPYLHQQDF EKLSQNLLVT SYMIYLMNWC DFKKSPFLIA EQDETVISLR EDIITSKHLC VIIDLYANHH KPPWIIDLN PQEKICVLRD FISKSRHVDT SSRSWNTSDL DFVIFYASLT YLRRGIIKQL RIRQVTEVID TTTMLRDNII V ENPPIKTG VLDIRGCIIY NLEEILSMNT KSASKKIFNL NSRPSVENHK YRRIGLNSSS CYKALNLSPL IQRYLPSGAQ RL FIGEGSG SMMLLYQSTL GQSISFYNSG IDGDYIPGQR ELKLFPSEYS IAEEDPSLTG KLKGLVVPLF NGRPETTWIG NLD SYEYII NRTAGRSIGL VHSDMESGID KNVEEILVEH SHLISIAINV MMEDGLLVSK IAYTPGFPIS RLFNMYRSYF GLVL VCFPV YSNPDSTEVY LLCLQKTVKT IVPPQKVLEH SNLHDEVNDQ GITSVIFKIK NSQSKQFHDD LKKYYQIDQP FFVPT KITS DEQVLLQAGL KLNGPEILKS EISYDIGSDI NTLRDTIIIM LNEAMNYFDD NRSPSHHLEP YPVLERTRIK TIMNCV TKK VIVYSLIKFK DTKSSELYHI KNNIRRKVLI LDFRSKLMTK TLPKGMQERR EKNGFKEVWI VDLSNREVKI WWKIIGY IS II

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 78.39032 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #3: ~{N}-[4-[(2~{S})-2-[2-[4-[2-(3-cyanophenyl)ethanoyl]piperazin-1-y...

MacromoleculeName: ~{N}-[4-[(2~{S})-2-[2-[4-[2-(3-cyanophenyl)ethanoyl]piperazin-1-yl]ethyl]piperidin-1-yl]sulfonylphenyl]-2-methyl-5-(trifluoromethyl)pyrazole-3-carboxamide
type: ligand / ID: 3 / Number of copies: 1 / Formula: A1E3H
Molecular weightTheoretical: 671.733 Da

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
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: INSILICO MODEL
Final reconstructionNumber classes used: 93063 / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1638544
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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