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- EMDB-55567: Structure of the Vesicular Stomatitis Virus L Protein in Complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-55567
TitleStructure of the Vesicular Stomatitis Virus L Protein in Complex with the Phosphoprotein and the Nucleoprotein
Map data
Sample
  • Complex: VSIV L:P:N complex
    • Complex: L:P complex
      • Protein or peptide: RNA-directed RNA polymerase L
      • Protein or peptide: Phosphoprotein
    • Complex: N0-P complex
      • Protein or peptide: Nucleoprotein
  • Ligand: ZINC ION
KeywordsVesicular stomatitis virus / L protein / P protein / phosphoprotein / nucleoprotein / N protein / single particle analysis / replication / virus / protein complex / N0-P complex / replication complex / VIRAL PROTEIN
Function / homology
Function and homology information


RNA replication / GDP polyribonucleotidyltransferase / RNA folding chaperone / phosphorylation / negative stranded viral RNA replication / helical viral capsid / viral transcription / virion component / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication ...RNA replication / GDP polyribonucleotidyltransferase / RNA folding chaperone / phosphorylation / negative stranded viral RNA replication / helical viral capsid / viral transcription / virion component / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ribonucleoprotein complex / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / host cell cytoplasm / metal ion binding / RNA binding / ATP binding
Similarity search - Function
Phosphoprotein, central domain / : / : / Vesiculovirus phosphoprotein / Virus-capping methyltransferase, C-terminal / Phosphoprotein, C-terminal domain, viral / RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / Rhabdovirus nucleocapsid ...Phosphoprotein, central domain / : / : / Vesiculovirus phosphoprotein / Virus-capping methyltransferase, C-terminal / Phosphoprotein, C-terminal domain, viral / RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Phosphoprotein / Nucleoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus strain San Juan
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBloyet LM / Whelan SPJ
Funding support United States, France, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI059371 United States
Agence Nationale de la Recherche (ANR)ANR-23-CE11-0001-01 France
CitationJournal: To Be Published
Title: Structure of the Vesicular Stomatitis Virus L Protein in Complex with the Phosphoprotein and the Nucleoprotein
Authors: Bloyet LM / Whelan SPJ
History
DepositionNov 4, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55567.png

Downloads & links

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Map

FileDownload / File: emd_55567.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 280 pix.
= 263.2 Å		0.94 Å/pix.
x 280 pix.
= 263.2 Å		0.94 Å/pix.
x 280 pix.
= 263.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.029227572 - 0.060330108
Average (Standard dev.)0.00010343011 (±0.0027063766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 263.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55567_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map post-processed by DeepEMhancer

Fileemd_55567_additional_1.map
AnnotationMap post-processed by DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55567_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_55567_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VSIV L:P:N complex

EntireName: VSIV L:P:N complex
Components
  • Complex: VSIV L:P:N complex
    • Complex: L:P complex
      • Protein or peptide: RNA-directed RNA polymerase L
      • Protein or peptide: Phosphoprotein
    • Complex: N0-P complex
      • Protein or peptide: Nucleoprotein
  • Ligand: ZINC ION

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Supramolecule #1: VSIV L:P:N complex

SupramoleculeName: VSIV L:P:N complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: L protein (full-length) in complex with P protein (1-106) and N protein (full-length)
Source (natural)Organism: Vesicular stomatitis Indiana virus strain San Juan
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: L:P complex

SupramoleculeName: L:P complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3
Details: L protein (full-length) in complex with a fragment of P (49-106)
Source (natural)Organism: Vesicular stomatitis Indiana virus strain San Juan

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Supramolecule #3: N0-P complex

SupramoleculeName: N0-P complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Details: N protein (full-length) in complex with a framgent of P (5-32)
Source (natural)Organism: Vesicular stomatitis Indiana virus strain San Juan

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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: Vesicular stomatitis Indiana virus strain San Juan
Molecular weightTheoretical: 241.339922 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: GPMEVHDFET DEFNDFNEDD YATREFLNPD ERMTYLNHAD YNLNSPLISD DIDNLIRKFN SLPIPSMWDS KNWDGVLEML TSCQANPIS TSQMHKWMGS WLMSDNHDAS QGYSFLHEVD KEAEITFDVV ETFIRGWGNK PIEYIKKERW TDSFKILAYL C QKFLDLHK ...String:
GPMEVHDFET DEFNDFNEDD YATREFLNPD ERMTYLNHAD YNLNSPLISD DIDNLIRKFN SLPIPSMWDS KNWDGVLEML TSCQANPIS TSQMHKWMGS WLMSDNHDAS QGYSFLHEVD KEAEITFDVV ETFIRGWGNK PIEYIKKERW TDSFKILAYL C QKFLDLHK LTLILNAVSE VELLNLARTF KGKVRRSSHG TNICRIRVPS LGPTFISEGW AYFKKLDILM DRNFLLMVKD VI IGRMQTV LSMVCRIDNL FSEQDIFSLL NIYRIGDKIV ERQGNFSYDL IKMVEPICNL KLMKLARESR PLVPQFPHFE NHI KTSVDE GAKIDRGIRF LHDQIMSVKT VDLTLVIYGS FRHWGHPFID YYTGLEKLHS QVTMKKDIDV SYAKALASDL ARIV LFQQF NDHKKWFVNG DLLPHDHPFK SHVKENTWPT AAQVQDFGDK WHELPLIKCF EIPDLLDPSI IYSDKSHSMN RSEVL KHVR MNPNTPIPSK KVLQTMLDTK ATNWKEFLKE IDEKGLDDDD LIIGLKGKER ELKLAGRFFS LMSWKLREYF VITEYL IKT HFVPMFKGLT MADDLTAVIK KMLDSSSGQG LKSYEAICIA NHIDYEKWNN HQRKLSNGPV FRVMGQFLGY PSLIERT HE FFEKSLIYYN GRPDLMRVHN NTLINSTSQR VCWQGQEGGL EGLRQKGWSI LNLLVIQREA KIRNTAVKVL AQGDNQVI C TQYKTKKSRN VVELQGALNQ MVSNNEKIMT AIKIGTGKLG LLINDDETMQ SADYLNYGKI PIFRGVIRGL ETKRWSRVT CVTNDQIPTC ANIMSSVSTN ALTVAHFAEN PINAMIQYNY FGTFARLLLM MHDPALRQSL YEVQDKIPGL HSSTFKYAML YLDPSIGGV SGMSLSRFLI RAFPDPVTES LSFWRFIHVH ARSEHLKEMS AVFGNPEIAK FRITHIDKLV EDPTSLNIAM G MSPANLLK TEVKKCLIES RQTIRNQVIK DATIYLYHEE DRLRSFLWSI NPLFPRFLSE FKSGTFLGVA DGLISLFQNS RT IRNSFKK KYHRELDDLI VRSEVSSLTH LGKLHLRRGS CKMWTCSATH ADTLRYKSWG RTVIGTTVPH PLEMLGPQHR KET PCAPCN TSGFNYVSVH CPDGIHDVFS SRGPLPAYLG SKTSESTSIL QPWERESKVP LIKRATRLRD AISWFVEPDS KLAM TILSN IHSLTGEEWT KRQHGFKRTG SALHRFSTSR MSHGGFASQS TAALTRLMAT TDTMRDLGDQ NFDFLFQATL LYAQI TTTV ARDGWITSCT DHYHIACKSC LRPIEEITLD SSMDYTPPDV SHVLKTWRNG EGSWGQEIKQ IYPLEGNWKN LAPAEQ SYQ VGRCIGFLYG DLAYRKSTHA EDSSLFPLSI QGRIRGRGFL KGLLDGLMRA SCCQVIHRRS LAHLKRPANA VYGGLIY LI DKLSVSPPFL SLTRSGPIRD ELETIPHKIP TSYPTSNRDM GVIVRNYFKY QCRLIEKGKY RSHYSQLWLF SDVLSIDF I GPFSISTTLL QILYKPFLSG KDKNELRELA NLSSLLRSGE GWEDIHVKFF TKDILLCPEE IRHACKFGIA KDNNKDMSY PPWGRESRGT ITTIPVYYTT TPYPKMLEMP PRIQNPLLSG IRLGQLPTGA HYKIRSILHG MGIHYRDFLS CGDGSGGMTA ALLRENVHS RGIFNSLLEL SGSVMRGASP EPPSALETLG GDKSRCVNGE TCWEYPSDLC DPRTWDYFLR LKAGLGLQID L IVMDMEVR DSSTSLKIET NVRNYVHRIL DEQGVLIYKT YGTYICESEK NAVTILGPMF KTVDLVQTEF SSSQTSEVYM VC KGLKKLI DEPNPDWSSI NESWKNLYAF QSSEQEFARA KKVSTYFTLT GIPSQFIPDP FVNIETMLQI FGVPTGVSHA AAL KSSDRP ADLLTISLFY MAIISYYNIN HIRVGPIPPN PPSDGIAQNV GIAITGISFW LSLMEKDIPL YQQCLAVIQQ SFPI RWEAI SVKGGYKQKW STRGDGLPKD TRISDSLAPI GNWIRSLELV RNQVRLNPFN KILFNQLCRT VDNHLKWSNL RKNTG MIEW INGRISKEDR SILMLKSDLH EENSWRD

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vesicular stomatitis Indiana virus strain San Juan
Molecular weightTheoretical: 47.463949 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSVTVKRIID NTVIVPKLPA NEDPVEYPAD YFRKSKEIPL YINTTKSLSD LRGYVYQGLK SGNVSIIHVN SYLYGALKDI RGKLDKDWS SFGINIGKAG DTIGIFDLVS LKALDGVLPD GVSDASRTSA DDKWLPLYLL GLYRVGRTQM PEYRKKLMDG L TNQCKMIN ...String:
MSVTVKRIID NTVIVPKLPA NEDPVEYPAD YFRKSKEIPL YINTTKSLSD LRGYVYQGLK SGNVSIIHVN SYLYGALKDI RGKLDKDWS SFGINIGKAG DTIGIFDLVS LKALDGVLPD GVSDASRTSA DDKWLPLYLL GLYRVGRTQM PEYRKKLMDG L TNQCKMIN EQFEPLVPEG RDIFDVWGND SNYTKIVAAV DMFFHMFKKH ECASFRYGTI VSRFKDCAAL ATFGHLCKIT GM STEDVTT WILNREVADE MVQMMLPGQE IDKADSYMPY LIDFGLSSKS PYSSVKNPAF HFWGQLTALL LRSTRARNAR QPD DIEYTS LTTAGLLYAY AVGSSADLAQ QFCVGDNKYT PDDSTGGLTT NAPPQGRDVV EWLGWFEDQN RKPTPDMMQY AKRA VMSLQ GLREKTIGKY AKSEFDK

UniProtKB: Nucleoprotein

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Macromolecule #3: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vesicular stomatitis Indiana virus strain San Juan
Molecular weightTheoretical: 13.054788 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDNLTKVREY LKSYSRLDQA VGEIDEIEAQ RAEKSNYELF QEDGVEEHTR PSYFQAADDS DTESEPEIED NQGLYVPDPE AEQVEGFIQ GPLDDYADED VDVVFTSGSG LEVLFQ

UniProtKB: Phosphoprotein

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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
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
SoftwareName: EPU (ver. 3.5.1)
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON IV (4k x 4k) / #0 - Number real images: 3881 / #0 - Average exposure time: 8.38 sec. / #0 - Average electron dose: 55.99 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON IV (4k x 4k) / #1 - Number real images: 6441 / #1 - Average exposure time: 7.27 sec. / #1 - Average electron dose: 54.38 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm

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Image processing

Image recording ID1
DetailsGain-corrected movies were aligned using cryoSPARC
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6) / Details: CTF estimation and correction with cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Software - details: 3D Flex / Details: 3D Flexible refinement / Number images used: 34000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)

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Atomic model buiding 1

Initial model
PDB IDChain

6u1x

source_name: PDB, initial_model_type: experimental model

3pmk

source_name: PDB, initial_model_type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.9.dev202410260116)
DetailsL-P from 6U1X was rigid-body fitted in the map. N0-P from 3PMK (chains D and O) was rigid-body fitted in the map after deletion of the C-loop (aa 342-374). The model was then locally edited and refined to introduce mutations and solve clashes.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9t53:
Structure of the Vesicular Stomatitis Virus L Protein in Complex with the Phosphoprotein and the Nucleoprotein

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