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- EMDB-44465: The structure of NiV L-P complex -

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Basic information

Entry
Database: EMDB / ID: EMD-44465
TitleThe structure of NiV L-P complex
Map data
Sample
  • Complex: Nipah virus the Large protein (L) with its cofactor phosphoprotein (P)
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ZINC ION
KeywordsRdRp complex / L-P complex / Nipah virus / VIRAL PROTEIN
Function / homology
Function and homology information


GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Transferases; Transferring one-carbon groups; Methyltransferases / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase 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: 2.26 Å
AuthorsHu S / Yang P / Abraham J
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Cell / Year: 2025
Title: Structural and functional analysis of the Nipah virus polymerase complex.
Authors: Side Hu / Heesu Kim / Pan Yang / Zishuo Yu / Barbara Ludeke / Shawna Mobilia / Junhua Pan / Margaret Stratton / Yuemin Bian / Rachel Fearns / Jonathan Abraham /
Abstract: Nipah virus (NiV) is a bat-borne, zoonotic RNA virus that is highly pathogenic in humans. The NiV polymerase, which mediates viral genome replication and mRNA transcription, is a promising drug ...Nipah virus (NiV) is a bat-borne, zoonotic RNA virus that is highly pathogenic in humans. The NiV polymerase, which mediates viral genome replication and mRNA transcription, is a promising drug target. We determined the cryoelectron microscopy (cryo-EM) structure of the NiV polymerase complex, comprising the large protein (L) and phosphoprotein (P), and performed structural, biophysical, and in-depth functional analyses of the NiV polymerase. The L protein assembles with a long P tetrameric coiled-coil that is capped by a bundle of ⍺-helices that we show are likely dynamic in solution. Docking studies with a known L inhibitor clarify mechanisms of antiviral drug resistance. In addition, we identified L protein features that are required for both transcription and RNA replication and mutations that have a greater impact on RNA replication than on transcription. Our findings have the potential to aid in the rational development of drugs to combat NiV infection.
History
DepositionApr 12, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44465.png

Downloads & links

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Map

FileDownload / File: emd_44465.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017325922 - 1.5831158
Average (Standard dev.)0.00035985804 (±0.013098404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_44465_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44465_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_44465_half_map_2.map
Projections & Slices
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Sample components

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Entire : Nipah virus the Large protein (L) with its cofactor phosphoprotein (P)

EntireName: Nipah virus the Large protein (L) with its cofactor phosphoprotein (P)
Components
  • Complex: Nipah virus the Large protein (L) with its cofactor phosphoprotein (P)
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ZINC ION

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Supramolecule #1: Nipah virus the Large protein (L) with its cofactor phosphoprotein (P)

SupramoleculeName: Nipah virus the Large protein (L) with its cofactor phosphoprotein (P)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: co-expressed and purified using the tag on L protein
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 580 kDa/nm

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Macromolecule #1: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 1 / Details: full length / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 257.59325 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADELSISDI IYPECHLDSP IVSGKLISAI EYAQLKHNQP SDDKRLSENI RLNLHGKRKS LYILRQSKQG NYIRNNVKNL KEFMHIAYP ECNNTLFSIT SQGMTSKLDN IMRKSFKAYN IISKKVIGML QNITRNLITQ DRRDEIINIH ECRRLGDLGK N MSQSKWYE ...String:
MADELSISDI IYPECHLDSP IVSGKLISAI EYAQLKHNQP SDDKRLSENI RLNLHGKRKS LYILRQSKQG NYIRNNVKNL KEFMHIAYP ECNNTLFSIT SQGMTSKLDN IMRKSFKAYN IISKKVIGML QNITRNLITQ DRRDEIINIH ECRRLGDLGK N MSQSKWYE CFLFWFTIKT EMRAVIKNSQ KPKFRSDSCI IHMRDKSTEI ILNPNLICIF KSDKTGKKCY YLTPEMVLMY CD VLEGRMM METTIKSDIK 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 LSGAYLEDDQ FNVSYSLKEK ETKQAGRLFA KMTYKM RAC QVIAEALIAS GVGKYFKENG MVKDEHELLK TLFQLSISSV PRGNSQGNDP QSINNIEKDF QCFKGVTTSV KDKKNDP FY KVKSALNNPC QADGVYHNMS PNIRNRYKCS NTSKSFLDYH TEFNPHNHYK SDNTEAAVLS KYEDNTGTKF DTVSAFLT T DLKKFCLNWR YESMAIFAER LDEIYGLPGF FNWMHKRLER SVIYVADPNC PPNIDKHMEL EETPEDDIFI HYPKGGIEG YSQKTWTIAT IPFLFLSAYE TNTRIAAIVQ GDNESIAITQ KVHPNLPYKV KKEICAKQAQ LYFERLRMNL RALGHNLKAT ETIISTHLF VYSKKIHYDG 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 SGLRKSGIQP RLVSRLSHHD YNQFLILNKL LSNRKQNDLI SSNTCSVDLA RALR SHMWR ELALGRVIYG LEVPDALEAM VGRYITGSLE CQICEQGNTM YGWFFVPRDS QLDQVDKEHS 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 DALAKTVAQT VLEIITKADK DVLKQHLA I DSDDNINSLI TEFLIVDPEL FALYLGQSIA IKWAFEIHHR RPRGRHTMVD LLSDLISNTS KHTYKVLSNA LSHPRVFKR FVNCGLLLPT QGPYLHQQDF EKLSQNLLVT SYMIYLMNWC DFKKYPFLIA EQDETVINLR EDIITSKHLC VIIDLYANHH KPPWIIDLN PQEKICVLRD FISKSRHMDT SSRSWNTSDL DFVIFYASLT YLRRGIIKQL RIRQVTEVVD TTTMLRDNII V ENPPIKTG VLDIRGCIIY NLEEILSMNT KSSSKKIFNL NSKPSVENHK YRRIGLNSSS CYKALNLSPL IQRYLPSGAQ RL FIGEGSG SMMLLYQSTL GQSISFYNSG IDGDYIPGQR ELKLFPSEYS IAEEDPSLAG KLKGLVVPLF NGRPETTWIG NLD SYEYII NRTAGRSIGL VHSDMESGID KNVEEILVEH SHLISIAINV MMEDGLLVSK IAYTPGFPIS RLFNMYRSYF GLVL VCFPV YSNPDSTEVY LLCLQKTVKT IIPPQRVLEH SDLHDEVNDQ GITSVIFKIK NSQSKQFHED LKKYYHIDQP FFVPT KITS DEQVLLQAGL KLNGPEILKS EISYDIGSDI NTLRDTIIIM LNEAMNYFDD NRSPSHHLEP YPVLERTRIK TIMNRV TKK VIVYSLIKFK DTKSSELYHI KNNIRRKVLI LDFRSKLMTK TLPKGMQERR EKSGFKEVWI 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 / Details: full length / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 78.141094 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDKLELVNDG LNIIDFIQKN QKEIQKTYGR SSIQQPSIKD RTKAWEDFLQ CTSGESEQVE GGMSKDDGGV ERRSLEDLSS TSPTDGTIG KRVSNTRDWA EGSDDIQLDP VVTDVVYHDH GGECTGYGFT SSPERGWSDH SSGANNGDVC LVSDAKVLSY A PEIAVSKE ...String:
MDKLELVNDG LNIIDFIQKN QKEIQKTYGR SSIQQPSIKD RTKAWEDFLQ CTSGESEQVE GGMSKDDGGV ERRSLEDLSS TSPTDGTIG KRVSNTRDWA EGSDDIQLDP VVTDVVYHDH GGECTGYGFT SSPERGWSDH SSGANNGDVC LVSDAKVLSY A PEIAVSKE DRETDLVHLE DKLSATGLNP TAIPFTPKNL SVPAKDSPVI AEHYYGLGVR EQNVDPQTNR NVNLDSIKLY TS DDEEADQ LEFEDEFAGS SSEVIVGISP EEEEPSSAGR KPIESVGHII EGQSTRDSLQ IKGNKPADAP GAGPKDSAVK EKS PQKRLP MLAEEFECSG SEDPIIQELL KENSFINSQQ GKDAQPLYYR GIEGSRSPDK TEITSDAVQT ANKQRPGTPM PKSR GIPIK KGTDEKYPSA GTENVPGSKS GATRHVRGSP PYQEGKSVNA ENVQLNVPTV VKETDKSEAN PADDNDSLDD KYIMP SDDF SNTFFPHDTD RLNYHADHLG DYDLETLCEE SVLMGVINSI KLINLDMRLN HIEEQVKEIP KIINKLESID RVLAKT NTA LSTIEGHLVS MMIMIPGKGK GERKGKSNPE LKPVIGRDVL EQQSLFSFDN VKNFRDGSLT NEPYGAAVQL RGDLILP EL NFEETNASQF VPMADDSSRD VVKTLIRTHI KDRELRSELI GYLNRAENDE EIQEIANTVN DIIDGNI

UniProtKB: Phosphoprotein

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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

Concentration0.7 mg/mL
BufferpH: 7.5
Details: 20 mM Tris-HC, 500 mM NaCl, 2 mM MgSO4, 1 mM DTT, pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1871392
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 477936
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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