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- EMDB-48649: Cryo-EM structure of a truncated Nipah virus (Malaysia Strain) L:... -

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Basic information

Entry
Database: EMDB / ID: EMD-48649
TitleCryo-EM structure of a truncated Nipah virus (Malaysia Strain) L:P complex
Map data
Sample
  • Complex: Complex of Nipah virus RNA polymerase L protein with its cofactor P protein
    • Protein or peptide: Phosphoprotein
    • Protein or peptide: RNA-directed RNA polymerase L
KeywordsRNA dependent RNA polymerase / Nipah virus / LP complex / VIRAL PROTEIN / TRANSFERASE
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 / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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 / 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 / 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 / Mononegavirus L protein 2-O-ribose methyltransferase ...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 / 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: 2.99 Å
AuthorsChen ZH / Liang B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI171413 United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structures of Nipah virus polymerases and high-throughput RdRp assay development enable anti-NiV drug discovery.
Authors: Zhenhang Chen / Jeanne Quirit Dudley / Colin Deniston / Cosmo Z Buffalo / Debjani Patra / Dongdong Cao / Julia Hunt / Ahmed Rohaim / Debapriya Sengupta / Lan Wen / Tiffany Tsang / Lili Xie / ...Authors: Zhenhang Chen / Jeanne Quirit Dudley / Colin Deniston / Cosmo Z Buffalo / Debjani Patra / Dongdong Cao / Julia Hunt / Ahmed Rohaim / Debapriya Sengupta / Lan Wen / Tiffany Tsang / Lili Xie / Michael DiDonato / Glen Spraggon / Matthew C Clifton / Nadine Jarrousse / Judith Straimer / Bo Liang /
Abstract: Transcription and replication of the Nipah virus (NiV) are driven by the large protein (L) together with its essential co-factor phosphoprotein (P). L encodes all the viral enzymatic functions, ...Transcription and replication of the Nipah virus (NiV) are driven by the large protein (L) together with its essential co-factor phosphoprotein (P). L encodes all the viral enzymatic functions, including RNA-dependent RNA polymerase (RdRp) activity, while the tetrameric P is multi-modular. Here, we investigate the molecular mechanism of the NiV polymerase and build tools for anti-NiV drug discovery. We analyze and compare multiple cryo-EM structures of both full-length and truncated NiV polymerases from the Malaysia and Bangladesh strains. We identify two conserved loops in the polyribonucleotidyltransferase (PRNTase) domain of L and the binding between RdRp-PRNTase and CD domains. To further assess the mechanism of NiV polymerase activity, we establish a highly sensitive radioactive-labeled RNA synthesis assay and identify a back-priming activity in the NiV polymerase as well as a fluorescence and luminescent-based non-radioactive polymerase assay to enable high-throughput screening for L protein inhibitors. The combination of structural analysis and the development of both high-sensitive and high-throughput biochemical assays will enable the identification of new direct-acting antiviral candidates for treating highly pathogenic henipaviruses.
History
DepositionJan 14, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48649.png

Downloads & links

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Map

FileDownload / File: emd_48649.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 355.968 Å		0.93 Å/pix.
x 384 pix.
= 355.968 Å		0.93 Å/pix.
x 384 pix.
= 355.968 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.927 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.1275198 - 1.6569675
Average (Standard dev.)0.0000872524 (±0.03136509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 355.968 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48649_half_map_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_48649_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of Nipah virus RNA polymerase L protein with its cofactor...

EntireName: Complex of Nipah virus RNA polymerase L protein with its cofactor P protein
Components
  • Complex: Complex of Nipah virus RNA polymerase L protein with its cofactor P protein
    • Protein or peptide: Phosphoprotein
    • Protein or peptide: RNA-directed RNA polymerase L

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Supramolecule #1: Complex of Nipah virus RNA polymerase L protein with its cofactor...

SupramoleculeName: Complex of Nipah virus RNA polymerase L protein with its cofactor P protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Details: A truncation of L and the full length of P protein of Nipah virus expressed from insect cell Spodoptera frugiperda
Source (natural)Organism: Henipavirus nipahense / Strain: Malaysia
Molecular weightTheoretical: 500 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: Henipavirus nipahense / Strain: Malaysia
Molecular weightTheoretical: 170.734672 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKSSHHHHHH HHHHGSSENL YFQSGSMADE LSISDIIYPE CHLDSPIVSG KLISAIEYAQ LRHNQPSDDK RLSENIRLNL HGKRKSLYI LRQSKQGDYI RNNIKNLKEF MHIAYPECNN ILFSITSQGM TSKLDNIMKK SFKAYNIISK KVIGMLQNIT R NLITQDRR ...String:
MKSSHHHHHH HHHHGSSENL YFQSGSMADE LSISDIIYPE CHLDSPIVSG KLISAIEYAQ LRHNQPSDDK RLSENIRLNL HGKRKSLYI LRQSKQGDYI RNNIKNLKEF MHIAYPECNN ILFSITSQGM TSKLDNIMKK SFKAYNIISK KVIGMLQNIT R NLITQDRR DEIINIHECR RLGDLGKNMS QSKWYECFLF WFTIKTEMRA VIKNSQKPKF RSDSCIIHMR DKSTEIILNP NL ICIFKSD KTGKKCYYLT PEMVLMYCDV LEGRMMMETT VKSDIKYQPL ISRSNALWGL IDPLFPVMGN RIYNIVSMIE PLV LALLQL KDEARILRGA FLHHCIKEMH QELSECGFTD QKIRSMFIDD LLSILNIDNI HLLAEFFSFF RTFGHPILEA KVAA EKVRE HMLADKVLEY APIMKAHAIF CGTIINGYRD RHGGAWPPLY LPAHASKHII RLKNSGESLT IDDCVKNWES FCGIQ FDCF MELKLDSDLS MYMKDKALSP IKDEWDSVYP REVLSYTPPK STEPRRLVDV FVNDENFDPY NMLEYVLSGA YLEDEQ FNV SYSLKEKETK QAGRLFAKMT YKMRACQVIA EALIASGVGK YFKENGMVKD EHELLKTLFQ LSISSVPRGN SQGNDPQ SI NNIERDFQYF KGVTTNVKDK KNNSFNKVKS ALNNPCQADG VHHNMSPNTR NRYKCSNTSK SFLDYHTEFN PHNHYKSD N TEAAVLSRYE DNTGTKFDTV SAFLTTDLKK FCLNWRYESM AIFAERLDEI YGLPGFFNWM HKRLERSVIY VADPNCPPN IDKHMELEKT PEDDIFIHYP KGGIEGYSQK TWTIATIPFL FLSAYETNTR IAAIVQGDNE SIAITQKVHP NLPYKVKKEI CAKQAQLYF ERLRMNLRAL GHNLKATETI ISTHLFIYSK KIHYDGAVLS QALKSMSRCC FWSETLVDET RSACSNISTT I AKAIENGL SRNVGYCINI LKVIQQLLIS TEFSINETLT LDVTSPISNN LDWLITAALI PAPIGGFNYL NLSRIFVRNI GD PVTASLA DLKRMIDHSI MTESVLQKVM NQEPGDASFL DWASDPYSGN LPDSQSITKT IKNITARTIL RNSPNPMLKG LFH DKSFDE DLELASFLMD RRVILPRAAH EILDNSLTGA REEIAGLLDT TKGLIRSGLR KSGLQPKLVS RLSHHDYNQF LILN KLLSN RRQNDLISSN TCSVDLARAL RSHMWRELAL GRVIYGLEVP DALEAMVGRY ITGSLECQIC EQGNTMYGWF FVPRD SQLD QVDREHSSIR VPYVGSSTDE RSDIKLGNVK RPTKALRSAI RIATVYTWAY GDNEECWYEA WYLASQRVNI DLDVLK AIT PVSTSNNLSH RLRDKSTQFK FAGSVLNRVS RYVNISNDNL DFRIEGEKVD TNLIYQQAML LGLSVLEGKF RLRLETD DY NGIYHLHVKD NCCVKEVADV GQVDAELPIP EYTEVDNNHL IYDPDPV

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense / Strain: Malaysia
Molecular weightTheoretical: 84.026422 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKSSWSHPQF EKGAMTGWSH PQFEKGSSAS WSHPQFEKGA ENLYFQSNGS MDKLELVNDG LNIIDFIQKN QKEIQKTYGR SSIQQPSIK DQTKAWEDFL QCTSGESEQV EGGMSKDDGD VERRNLEDLS STSPTDGTIG KRVSNTRDWA EGSDDIQLDP V VTDVVYHD ...String:
MKSSWSHPQF EKGAMTGWSH PQFEKGSSAS WSHPQFEKGA ENLYFQSNGS MDKLELVNDG LNIIDFIQKN QKEIQKTYGR SSIQQPSIK DQTKAWEDFL QCTSGESEQV EGGMSKDDGD VERRNLEDLS STSPTDGTIG KRVSNTRDWA EGSDDIQLDP V VTDVVYHD HGGECTGYGF TSSPERGWSD YTSGANNGNV CLVSDAKMLS YAPEIAVSKE DRETDLVHLE NKLSTTGLNP TA VPFTLRN LSDPAKDSPV IAEHYYGLGV KEQNVGPQTS RNVNLDSIKL YTSDDEEADQ LEFEDEFAGS SSEVIVGISP EDE EPSSVG GKPNESIGRT IEGQSIRDNL QAKDNKSTDV PGAGPKDSAV KEEPPQKRLP MLAEEFECSG SEDPIIRELL KENS LINCQ QGKDAQPPYH WSIERSISPD KTEIVNGAVQ TADRQRPGTP MPKSRGIPIK KGTDAKYPSA GTENVPGSKS GATRH VRGS PPYQEGKSVN AENVQLNAST AVKETDKSEV NPVDDNDSLD DKYIMPSDDF SNTFFPHDTD RLNYHADHLG DYDLET LCE ESVLMGVINS IKLINLDMRL NHIEEQVKEI PKIINKLESI DRVLAKTNTA LSTIEGHLVS MMIMIPGKGK GERKGKN NP ELKPVIGRDI LEQQSLFSFD NVKNFRDGSL TNEPYGAAVQ LREDLILPEL NFEETNASQF VPMADDSSRD VIKTLIRT H IKDRELRSEL IGYLNKAEND EEIQEIANTV NDIIDGNI

UniProtKB: Phosphoprotein

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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

Concentration0.9 mg/mL
BufferpH: 7.6
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 173715
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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