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- EMDB-45782: Cryo-EM structure of the Nipah virus (Malaysia Strain) L:P complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45782
TitleCryo-EM structure of the 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 / 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: 2.92 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: To Be Published
Title: Cryo-EM structures of Nipah virus polymerase complexes
Authors: Chen ZH / Liang B
History
DepositionJul 16, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45782.png

Downloads & links

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Map

FileDownload / File: emd_45782.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.)
0.81 Å/pix.
x 480 pix.
= 388.32 Å		0.81 Å/pix.
x 480 pix.
= 388.32 Å		0.81 Å/pix.
x 480 pix.
= 388.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.809 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.405
Minimum - Maximum-2.1991196 - 3.5464017
Average (Standard dev.)0.00067368685 (±0.06749339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 388.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45782_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_45782_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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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: all
Details: Full length of L and P protein of Nipah virus expressed from insect cell Spodoptera frugiperda.
Source (natural)Organism: Henipavirus nipahense / Strain: Malaysia
Molecular weightTheoretical: 570 KDa

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Macromolecule #1: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
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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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: 260.638609 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 IYDPDPVSEI DCSRLSNQES KSRELDFPLW STEELHDV L AKTVAQTVLE IITKADKDVL KQHLAIDSDD NINSLITEFL IVDPELFALY LGQSISIKWA FEIHHRRPRG RHTMVDLLS DLVSNTSKHT YKVLSNALSH PRVFKRFVNC GLLLPTQGPY LHQQDFEKLS QNLLVTSYMI YLMNWCDFKK SPFLIAEQDE TVISLREDI ITSKHLCVII DLYANHHKPP WIIDLNPQEK ICVLRDFISK SRHVDTSSRS WNTSDLDFVI FYASLTYLRR G IIKQLRIR QVTEVIDTTT MLRDNIIVEN PPIKTGVLDI RGCIIYNLEE ILSMNTKSAS KKIFNLNSRP SVENHKYRRI GL NSSSCYK ALNLSPLIQR YLPSGAQRLF IGEGSGSMML LYQSTLGQSI SFYNSGIDGD YIPGQRELKL FPSEYSIAEE DPS LTGKLK GLVVPLFNGR PETTWIGNLD SYEYIINRTA GRSIGLVHSD MESGIDKNVE EILVEHSHLI SIAINVMMED GLLV SKIAY TPGFPISRLF NMYRSYFGLV LVCFPVYSNP DSTEVYLLCL QKTVKTIVPP QKVLEHSNLH DEVNDQGITS VIFKI KNSQ SKQFHDDLKK YYQIDQPFFV PTKITSDEQV LLQAGLKLNG PEILKSEISY DIGSDINTLR DTIIIMLNEA MNYFDD NRS PSHHLEPYPV LERTRIKTIM NCVTKKVIVY SLIKFKDTKS SELYHIKNNI RRKVLILDFR SKLMTKTLPK GMQERRE KN GFKEVWIVDL SNREVKIWWK IIGYISII

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

Concentration0.7 mg/mL
BufferpH: 7.6
Component:
ConcentrationNameFormula
30.0 mMtris(hydroxymethyl)aminomethane-HCl
300.0 mMsodium chlorideNaCl
1.0 mMtris(2-carboxyethyl)phosphine
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: PDB ENTRY
PDB model - PDB ID:

6v85

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 258905
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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