[English] 日本語
Yorodumi
- EMDB-3872: Cryo-electron tomogram of Ebola virus virus-like particles -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3872
TitleCryo-electron tomogram of Ebola virus virus-like particles
Map dataA 4x binned representative tomogram of recombinant virus-like particles from Ebola virus nucleoprotein, VP24, VP35, VP40.
Sample
  • Virus: Ebola virus - Mayinga, Zaire, 1976
    • Protein or peptide: Ebola virus nucleoprotein
    • Protein or peptide: Ebola virus VP24
    • Protein or peptide: Ebola Virus VP35
    • Protein or peptide: Ebola Virus VP40
Biological speciesEbola virus - Mayinga, Zaire, 1976
Methodelectron tomography / cryo EM
AuthorsWan W / Kolesnikova L / Clarke M / Koehler A / Noda T / Becker S / Briggs JAG
Funding support Germany, 3 items
OrganizationGrant numberCountry
European Research CouncilERC-CoG-648432 MEMBRANEFUSION Germany
German Research FoundationSonderforschungsbereich 1021 Germany
European Molecular Biology OrganizationALTF 748-2014 Germany
CitationJournal: Nature / Year: 2017
Title: Structure and assembly of the Ebola virus nucleocapsid.
Authors: William Wan / Larissa Kolesnikova / Mairi Clarke / Alexander Koehler / Takeshi Noda / Stephan Becker / John A G Briggs /
Abstract: Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles ...Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles virus, and respiratory syncytial virus. Mononegaviruses have non-segmented, single-stranded negative-sense RNA genomes that are encapsidated by nucleoprotein and other viral proteins to form a helical nucleocapsid. The nucleocapsid acts as a scaffold for virus assembly and as a template for genome transcription and replication. Insights into nucleoprotein-nucleoprotein interactions have been derived from structural studies of oligomerized, RNA-encapsidating nucleoprotein, and cryo-electron microscopy of nucleocapsid or nucleocapsid-like structures. There have been no high-resolution reconstructions of complete mononegavirus nucleocapsids. Here we apply cryo-electron tomography and subtomogram averaging to determine the structure of Ebola virus nucleocapsid within intact viruses and recombinant nucleocapsid-like assemblies. These structures reveal the identity and arrangement of the nucleocapsid components, and suggest that the formation of an extended α-helix from the disordered carboxy-terminal region of nucleoprotein-core links nucleoprotein oligomerization, nucleocapsid condensation, RNA encapsidation, and accessory protein recruitment.
History
DepositionSep 13, 2017-
Header (metadata) releaseNov 22, 2017-
Map releaseNov 22, 2017-
UpdateDec 4, 2019-
Current statusDec 4, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3872.png

Downloads & links

-
Map

FileDownload / File: emd_3872.map.gz / Format: CCP4 / Size: 491.7 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationA 4x binned representative tomogram of recombinant virus-like particles from Ebola virus nucleoprotein, VP24, VP35, VP40.
Voxel sizeX=Y=Z: 7.12 Å
Density
Minimum - Maximum-1934 - 1149
Average (Standard dev.)35.18454 (±27.61048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00113
Dimensions927927300
Spacing927927300
CellA: 6600.2397 Å / B: 6600.2397 Å / C: 2136.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z7.127.127.12
M x/y/z927927300
origin x/y/z0.0000.0000.000
length x/y/z6600.2406600.2402136.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS00113
NC/NR/NS927927300
D min/max/mean-1934.0001149.00035.185

-
Supplemental data

-
Sample components

-
Entire : Ebola virus - Mayinga, Zaire, 1976

EntireName: Ebola virus - Mayinga, Zaire, 1976
Components
  • Virus: Ebola virus - Mayinga, Zaire, 1976
    • Protein or peptide: Ebola virus nucleoprotein
    • Protein or peptide: Ebola virus VP24
    • Protein or peptide: Ebola Virus VP35
    • Protein or peptide: Ebola Virus VP40

-
Supramolecule #1: Ebola virus - Mayinga, Zaire, 1976

SupramoleculeName: Ebola virus - Mayinga, Zaire, 1976 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Recombinantly expressed virus-like particles produced by expression of nucleoprotein, VP24, VP35, VP40.
NCBI-ID: 128952 / Sci species name: Ebola virus - Mayinga, Zaire, 1976 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host systemOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T
Virus shellShell ID: 1 / Name: Nucleocapsid / Diameter: 280.0 Å

-
Macromolecule #1: Ebola virus nucleoprotein

MacromoleculeName: Ebola virus nucleoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDSRPQKIWM APSLTESDMD YHKILTAGLS VQQGIVRQRV IPVYQVNNLE EICQLIIQAF EAGVDFQES ADSFLLMLCL HHAYQGDYKL FLESGAVKYL EGHGFRFEVK KRDGVKRLEE L LPAVSSGK NIKRTLAAMP EEETTEANAG QFLSFASLFL PKLVVGEKAC ...String:
MDSRPQKIWM APSLTESDMD YHKILTAGLS VQQGIVRQRV IPVYQVNNLE EICQLIIQAF EAGVDFQES ADSFLLMLCL HHAYQGDYKL FLESGAVKYL EGHGFRFEVK KRDGVKRLEE L LPAVSSGK NIKRTLAAMP EEETTEANAG QFLSFASLFL PKLVVGEKAC LEKVQRQIQV HA EQGLIQY PTAWQSVGHM MVIFRLMRTN FLIKFLLIHQ GMHMVAGHDA NDAVISNSVA QAR FSGLLI VKTVLDHILQ KTERGVRLHP LARTAKVKNE VNSFKAALSS LAKHGEYAPF ARLL NLSGV NNLEHGLFPQ LSAIALGVAT AHGSTLAGVN VGEQYQQLRE AATEAEKQLQ QYAES RELD HLGLDDQEKK ILMNFHQKKN EISFQQTNAM VTLRKERLAK LTEAITAASL PKTSGH YDD DDDIPFPGPI NDDDNPGHQD DDPTDSQDTT IPDVVVDPDD GSYGEYQSYS ENGMNAP DD LVLFDLDEDD EDTKPVPNRS TKGGQQKNSQ KGQHIEGRQT QSRPIQNVPG PHRTIHHA S APLTDNDRRN EPSGSTSPRM LTPINEEADP LDDADDETSS LPPLESDDEE QDRDGTSNR TPTVAPPAPV YRDHSEKKEL PQDEQQDQDH TQEARNQDSD NTQSEHSFEE MYRHILRSQG PFDAVLYYH MMKDEPVVFS TSDGKEYTYP DSLEEEYPPW LTEKEAMNEE NRFVTLDGQQ F YWPVMNHK NKFMAILQHH Q

-
Macromolecule #2: Ebola virus VP24

MacromoleculeName: Ebola virus VP24 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAKATGRYNL ISPKKDLEKG VVLSDLCNFL VSQTIQGWKV YWAGIEFDVT HKGMALLHRL KTNDFAPAW SMTRNLFPHL FQNPNSTIES PLWALRVILA AGIQDQLIDQ SLIEPLAGAL G LISDWLLT TNTNHFNMRT QRVKEQLSLK MLSLIRSNIL KFINKLDALH ...String:
MAKATGRYNL ISPKKDLEKG VVLSDLCNFL VSQTIQGWKV YWAGIEFDVT HKGMALLHRL KTNDFAPAW SMTRNLFPHL FQNPNSTIES PLWALRVILA AGIQDQLIDQ SLIEPLAGAL G LISDWLLT TNTNHFNMRT QRVKEQLSLK MLSLIRSNIL KFINKLDALH VVNYNGLLSS IE IGTQNHT IIITRTNMGF LVELQEPDKS AMNRMKPGPA KFSLLHESTL KAFTQGSSTR MQS LILEFN SSLAI

-
Macromolecule #3: Ebola Virus VP35

MacromoleculeName: Ebola Virus VP35 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTTRTKGRGH TAATTQNDRM PGPELSGWIS EQLMTGRIPV SDIFCDIENN PGLCYASQMQ QTKPNPKTR NSQTQTDPIC NHSFEEVVQT LASLATVVQQ QTIASESLEQ RITSLENGLK P VYDMAKTI SSLNRVCAEM VAKYDLLVMT TGRATATAAA TEAYWAEHGQ ...String:
MTTRTKGRGH TAATTQNDRM PGPELSGWIS EQLMTGRIPV SDIFCDIENN PGLCYASQMQ QTKPNPKTR NSQTQTDPIC NHSFEEVVQT LASLATVVQQ QTIASESLEQ RITSLENGLK P VYDMAKTI SSLNRVCAEM VAKYDLLVMT TGRATATAAA TEAYWAEHGQ PPPGPSLYEE SA IRGKIES RDETVPQSVR EAFNNLNSTT SLTEENFGKP DISAKDLRNI MYDHLPGFGT AFH QLVQVI CKLGKDSNSL DIIHAEFQAS LAEGDSPQCA LIQITKRVPI FQDAAPPVIH IRSR GDIPR ACQKSLRPVP PSPKIDRGWV CVFQLQDGKT LGLKI

-
Macromolecule #4: Ebola Virus VP40

MacromoleculeName: Ebola Virus VP40 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRRVILPTAP PEYMEAIYPV RSNSTIARGG NSNTGFLTPE SVNGDTPSNP LRPIADDTID HASHTPGSV SSAFILEAMV NVISGPKVLM KQIPIWLPLG VADQKTYSFD STTAAIMLAS Y TITHFGKA TNPLVRVNRL GPGIPDHPLR LLRIGNQAFL QEFVLPPVQL ...String:
MRRVILPTAP PEYMEAIYPV RSNSTIARGG NSNTGFLTPE SVNGDTPSNP LRPIADDTID HASHTPGSV SSAFILEAMV NVISGPKVLM KQIPIWLPLG VADQKTYSFD STTAAIMLAS Y TITHFGKA TNPLVRVNRL GPGIPDHPLR LLRIGNQAFL QEFVLPPVQL PQYFTFDLTA LK LITQPLP AATWTDDTPT GSNGALRPGI SFHPKLRPIL LPNKSGKKGN SADLTSPEKI QAI MTSLQD FKIVPIDPTK NIMGIEVPET LVHKLTGKKV TSKNGQPIIP VLLPKYIGLD PVAP GDLTM VITQDCDTCH SPASLPAVIE K

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statehelical array

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloridesodium chloride
0.1 mMEDTAEthylenediaminetetraacetic acidethylenediaminetetraacetic acid
50.0 mMTris-HClTristrisaminomethane hydrochloride
GridModel: C-flat 2/1 3C / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK II
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: UMC Utrecht / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: -10 eV / Energy filter - Upper energy threshold: 10 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3708 pixel / Digitization - Dimensions - Height: 3708 pixel / Digitization - Frames/image: 1-5 / Average exposure time: 2.3 sec. / Average electron dose: 3.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4)defocus determination
CTFPHASEFLIPCTF-correction
Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41
DetailsFrames were aligned using K2Align software, based off the MotionCorr algorithm. Tomograms were reconstructed with IMOD, using stripwise CTF-correction and weighted back projection.

+
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