[English] 日本語
Yorodumi
- EMDB-20614: Structure of the Vesicular Stomatitis Virus L Protein in Complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20614
TitleStructure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor (3.0 A resolution)
Map datafiltered, sharpened
Sample
  • Complex: VSV L:P
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ZINC ION
KeywordsVesicular stomatitis virus / RNA-dependent RNA polymerase / L protein / P protein / phosphoprotein / single particle analysis / transcription / replication / virus / viral / RdRp / PRNTase / nonsegmented negative-sense RNA viruses / VIRAL PROTEIN
Function / homology
Function and homology information


NNS virus cap methyltransferase / RNA folding chaperone / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / phosphorylation / viral genome replication / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...NNS virus cap methyltransferase / RNA folding chaperone / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / phosphorylation / viral genome replication / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / ATP binding / metal ion 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 / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus ...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 / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesVesicular stomatitis virus / Vesicular stomatitis Indiana virus (strain San Juan)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsJenni S / Bloyet LM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R37 AI059371 United States
CitationJournal: Cell Rep / Year: 2020
Title: Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor.
Authors: Simon Jenni / Louis-Marie Bloyet / Ruben Diaz-Avalos / Bo Liang / Sean P J Whelan / Nikolaus Grigorieff / Stephen C Harrison /
Abstract: The large (L) proteins of non-segmented, negative-strand RNA viruses are multifunctional enzymes that produce capped, methylated, and polyadenylated mRNA and replicate the viral genome. A ...The large (L) proteins of non-segmented, negative-strand RNA viruses are multifunctional enzymes that produce capped, methylated, and polyadenylated mRNA and replicate the viral genome. A phosphoprotein (P), required for efficient RNA-dependent RNA polymerization from the viral ribonucleoprotein (RNP) template, regulates the function and conformation of the L protein. We report the structure of vesicular stomatitis virus L in complex with its P cofactor determined by electron cryomicroscopy at 3.0 Å resolution, enabling us to visualize bound segments of P. The contacts of three P segments with multiple L domains show how P induces a closed, compact, initiation-competent conformation. Binding of P to L positions its N-terminal domain adjacent to a putative RNA exit channel for efficient encapsidation of newly synthesized genomes with the nucleoprotein and orients its C-terminal domain to interact with an RNP template. The model shows that a conserved tryptophan in the priming loop can support the initiating 5' nucleotide.
History
DepositionAug 17, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseJan 22, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6u1x
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20614.png

Downloads & links

-
Map

FileDownload / File: emd_20614.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfiltered, sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 400 pix.
= 388. Å		0.97 Å/pix.
x 400 pix.
= 388. Å		0.97 Å/pix.
x 400 pix.
= 388. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.45932153 - 0.81560034
Average (Standard dev.)-0.0043358 (±0.03316188)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 388.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.970.970.97
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z388.000388.000388.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.4590.816-0.004

-
Supplemental data

-
Mask #1

Fileemd_20614_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: filtered

Fileemd_20614_additional_1.map
Annotationfiltered
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: filtered, sharpened, calculated on fine grid

Fileemd_20614_additional_2.map
Annotationfiltered, sharpened, calculated on fine grid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: filtered, sharpened, calculated on fine grid, boxed

Fileemd_20614_additional_3.map
Annotationfiltered, sharpened, calculated on fine grid, boxed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map1, unmodified

Fileemd_20614_half_map_1.map
Annotationhalf map1, unmodified
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map2, unmodified

Fileemd_20614_half_map_2.map
Annotationhalf map2, unmodified
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : VSV L:P

EntireName: VSV L:P
Components
  • Complex: VSV L:P
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ZINC ION

-
Supramolecule #1: VSV L:P

SupramoleculeName: VSV L:P / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: L protein (full-length) in complex with P protein (35-106)
Source (natural)Organism: Vesicular stomatitis virus
Molecular weightTheoretical: 240 KDa

-
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)
Strain: San Juan
Molecular weightTheoretical: 241.313859 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEVHDFETDE FNDFNEDDYA TREFLNPDER MTYLNHADYN LNSPLISDDI DNLIRKFNSL PIPSMWDSKN WDGVLEMLTS CQANPISTS QMHKWMGSWL MSDNHDASQG YSFLHEVDKE AEITFDVVET FIRGWGNKPI EYIKKERWTD SFKILAYLCQ K FLDLHKLT ...String:
MEVHDFETDE FNDFNEDDYA TREFLNPDER MTYLNHADYN LNSPLISDDI DNLIRKFNSL PIPSMWDSKN WDGVLEMLTS CQANPISTS QMHKWMGSWL MSDNHDASQG YSFLHEVDKE AEITFDVVET FIRGWGNKPI EYIKKERWTD SFKILAYLCQ K FLDLHKLT LILNAVSEVE LLNLARTFKG KVRRSSHGTN ICRIRVPSLG PTFISEGWAY FKKLDILMDR NFLLMVKDVI IG RMQTVLS MVCRIDNLFS EQDIFSLLNI YRIGDKIVER QGNFSYDLIK MVEPICNLKL MKLARESRPL VPQFPHFENH IKT SVDEGA KIDRGIRFLH DQIMSVKTVD LTLVIYGSFR HWGHPFIDYY TGLEKLHSQV TMKKDIDVSY AKALASDLAR IVLF QQFND HKKWFVNGDL LPHDHPFKSH VKENTWPTAA QVQDFGDKWH ELPLIKCFEI PDLLDPSIIY SDKSHSMNRS EVLKH VRMN PNTPIPSKKV LQTMLDTKAT NWKEFLKEID EKGLDDDDLI IGLKGKEREL KLAGRFFSLM SWKLREYFVI TEYLIK THF VPMFKGLTMA DDLTAVIKKM LDSSSGQGLK SYEAICIANH IDYEKWNNHQ RKLSNGPVFR VMGQFLGYPS LIERTHE FF EKSLIYYNGR PDLMRVHNNT LINSTSQRVC WQGQEGGLEG LRQKGWTILN LLVIQREAKI RNTAVKVLAQ GDNQVICT Q YKTKKSRNVV ELQGALNQMV SNNEKIMTAI KIGTGKLGLL INDDETMQSA DYLNYGKIPI FRGVIRGLET KRWSRVTCV TNDQIPTCAN IMSSVSTNAL TVAHFAENPI NAMIQYNYFG TFARLLLMMH DPALRQSLYE VQDKIPGLHS STFKYAMLYL DPSIGGVSG MSLSRFLIRA FPDPVTESLS FWRFIHVHAR SEHLKEMSAV FGNPEIAKFR ITHIDKLVED PTSLNIAMGM S PANLLKTE VKKCLIESRQ TIRNQVIKDA TIYLYHEEDR LRSFLWSINP LFPRFLSEFK SGTFLGVADG LISLFQNSRT IR NSFKKKY HRELDDLIVR SEVSSLTHLG KLHLRRGSCK MWTCSATHAD TLRYKSWGRT VIGTTVPHPL EMLGPQHRKE TPC APCNTS GFNYVSVHCP DGIHDVFSSR GPLPAYLGSK TSESTSILQP WERESKVPLI KRATRLRDAI SWFVEPDSKL AMTI LSNIH SLTGEEWTKR QHGFKRTGSA LHRFSTSRMS HGGFASQSTA ALTRLMATTD TMRDLGDQNF DFLFQATLLY AQITT TVAR DGWITSCTDH YHIACKSCLR PIEEITLDSS MDYTPPDVSH VLKTWRNGEG SWGQEIKQIY PLEGNWKNLA PAEQSY QVG RCIGFLYGDL AYRKSTHAED SSLFPLSIQG RIRGRGFLKG LLDGLMRASC CQVIHRRSLA HLKRPANAVY GGLIYLI DK LSVSPPFLSL TRSGPIRDEL ETIPHKIPTS YPTSNRDMGV IVRNYFKYQC RLIEKGKYRS HYSQLWLFSD VLSIDFIG P FSISTTLLQI LYKPFLSGKD KNELRELANL SSLLRSGEGW EDIHVKFFTK DILLCPEEIR HACKFGIAKD NNKDMSYPP WGRESRGTIT TIPVYYTTTP YPKMLEMPPR IQNPLLSGIR LGQLPTGAHY KIRSILHGMG IHYRDFLSCG DGSGGMTAAL LRENVHSRG IFNSLLELSG SVMRGASPEP PSALETLGGD KSRCVNGETC WEYPSDLCDP RTWDYFLRLK AGLGLQIDLI V MDMEVRDS STSLKIETNV RNYVHRILDE QGVLIYKTYG TYICESEKNA VTILGPMFKT VDLVQTEFSS SQTSEVYMVC KG LKKLIDE PNPDWSSINE SWKNLYAFQS SEQEFARAKK VSTYFTLTGI PSQFIPDPFV NIETMLQIFG VPTGVSHAAA LKS SDRPAD LLTISLFYMA IISYYNINHI RVGPIPPNPP SDGIAQNVGI AITGISFWLS LMEKDIPLYQ QCLAVIQQSF PIRW EAVSV KGGYKQKWST RGDGLPKDTR ISDSLAPIGN WIRSLELVRN QVRLNPFNEI LFNQLCRTVD NHLKWSNLRR NTGMI EWIN RRISKEDRSI LMLKSDLHEE NSWRD

UniProtKB: RNA-directed RNA polymerase L

-
Macromolecule #2: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vesicular stomatitis Indiana virus (strain San Juan)
Strain: San Juan
Molecular weightTheoretical: 29.941982 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDNLTKVREY LKSYSRLDQA VGEIDEIEAQ RAEKSNYELF QEDGVEEHTK PSYFQAADDS DTESEPEIED NQGLYAQDPE AEQVEGFIQ GPLDDYADEE VDVVFTSDWK PPELESDEHG KTLRLTSPEG LSGEQKSQWL STIKAVVQSA KYWNLAECTF E ASGEGVIM ...String:
MDNLTKVREY LKSYSRLDQA VGEIDEIEAQ RAEKSNYELF QEDGVEEHTK PSYFQAADDS DTESEPEIED NQGLYAQDPE AEQVEGFIQ GPLDDYADEE VDVVFTSDWK PPELESDEHG KTLRLTSPEG LSGEQKSQWL STIKAVVQSA KYWNLAECTF E ASGEGVIM KERQITPDVY KVTPVMNTHP SQSEAVSDVW SLSKTSMTFQ PKKASLQPLT ISLDELFSSR GEFISVGGDG RM SHKEAIL LGLRYKKLYN QARVKYSL

UniProtKB: Phosphoprotein

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 3 / Number real images: 3307 / Average exposure time: 5.0 sec. / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsMovies were gain-corrected and aligned using cisTEM.
Particle selectionNumber selected: 246825 / Details: Resolution limit for picking: 2 nm
Startup modelType of model: EMDB MAP
EMDB ID:

6337

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. X) / Software - details: Part of cisTEM
Details: Refinement and classification were limited to a resolution of 0.4 nm to produce unbiased resolution estimate at final estimate resolution.
Number images used: 83979
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. X) / Software - details: Part of cisTEM
Details: A global search was performed at 0.8 nm resolution.
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. X) / Software - details: Part of cisTEM
Final 3D classificationNumber classes: 2 / Avg.num./class: 42304 / Software - Name: FREALIGN (ver. X) / Software - details: Part of cisTEM
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5a22


Chain - Chain ID: A / Chain - Residue range: 35-2109 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 70.6 / Target criteria: CC + restraints
Output model

PDB-6u1x:
Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor (3.0 A resolution)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more