[English] 日本語
Yorodumi
- EMDB-50039: Coxsackievirus A9 bound with compound 14 (CL275) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50039
TitleCoxsackievirus A9 bound with compound 14 (CL275)
Map dataDensity map of Coxsackievirus A9 bound with CL275 obtained by cryoEM and single-particle processing in cryoSPARC at global resolution of 2.31 A.
Sample
  • Virus: Coxsackievirus A9
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
  • Ligand: 4-[(4-methylpiperazin-1-yl)methyl]-N-[[4-(trifluoromethyl)phenyl]methyl]aniline
  • Ligand: MYRISTIC ACID
KeywordsAntiviral / capsid stabilizer / hydrophobic pocket / cryoEM / VIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHuman coxsackievirus A9 (strain Griggs) / Coxsackievirus A9
Methodsingle particle reconstruction / cryo EM / Resolution: 2.31 Å
AuthorsPlavec Z / Butcher SJ / Mitchell C / Buckner C
Funding support Finland, 3 items
OrganizationGrant numberCountry
Academy of Finland315950 Finland
Sigrid Juselius Foundation95-7202-38 Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionApr 8, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50039.png

Downloads & links

-
Map

FileDownload / File: emd_50039.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of Coxsackievirus A9 bound with CL275 obtained by cryoEM and single-particle processing in cryoSPARC at global resolution of 2.31 A.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 450 pix.
= 436.5 Å		0.97 Å/pix.
x 450 pix.
= 436.5 Å		0.97 Å/pix.
x 450 pix.
= 436.5 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 AUTHOR: 0.25
Minimum - Maximum-0.47981676 - 1.2937583
Average (Standard dev.)0.019600939 (±0.11381315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 436.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Density half map of Coxsackievirus A9 bound with...

Fileemd_50039_half_map_1.map
AnnotationDensity half map of Coxsackievirus A9 bound with CL275 obtained by cryoEM and single-particle processing in cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Density half map of Coxsackievirus A9 bound with...

Fileemd_50039_half_map_2.map
AnnotationDensity half map of Coxsackievirus A9 bound with CL275 obtained by cryoEM and single-particle processing in cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Coxsackievirus A9

EntireName: Coxsackievirus A9
Components
  • Virus: Coxsackievirus A9
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
  • Ligand: 4-[(4-methylpiperazin-1-yl)methyl]-N-[[4-(trifluoromethyl)phenyl]methyl]aniline
  • Ligand: MYRISTIC ACID

-
Supramolecule #1: Coxsackievirus A9

SupramoleculeName: Coxsackievirus A9 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Coxsackievirus A9 was propagated on green monkey kidney cells and purified on a sucrose gradient.
NCBI-ID: 12067 / Sci species name: Coxsackievirus A9 / Sci species strain: Griggs / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8 MDa
Virus shellShell ID: 1 / Name: icosahedral capsid / Diameter: 300.0 Å / T number (triangulation number): 1

-
Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human coxsackievirus A9 (strain Griggs) / Strain: Griggs / Tissue: kidney
Molecular weightTheoretical: 32.053998 KDa
SequenceString: GDVEEAIERA VVHVADTMRS GPSNSASVPA LTAVETGHTS QVTPSDTMQT RHVKNYHSRS ESTVENFLGR SACVYMEEYK TTDNDVNKK FVAWPINTKQ MVQMRRKLEM FTYLRFDMEV TFVITSRQDP GTTLAQDMPV LTHQIMYVPP GGPIPAKVDD Y AWQTSTNP ...String:
GDVEEAIERA VVHVADTMRS GPSNSASVPA LTAVETGHTS QVTPSDTMQT RHVKNYHSRS ESTVENFLGR SACVYMEEYK TTDNDVNKK FVAWPINTKQ MVQMRRKLEM FTYLRFDMEV TFVITSRQDP GTTLAQDMPV LTHQIMYVPP GGPIPAKVDD Y AWQTSTNP SIFWTEGNAP ARMSIPFISI GNAYSNFYDG WSNFDQRGSY GYNTLNNLGH IYVRHVSGSS PHPITSTIRV YF KPKHTRA WVPRPPRLCQ YKKAFSVDFT PTPITDTRKD INTVTT

UniProtKB: Genome polyprotein

-
Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human coxsackievirus A9 (strain Griggs) / Strain: Griggs / Tissue: kidney
Molecular weightTheoretical: 27.791363 KDa
SequenceString: SDRVRSITLG NSTITTQECA NVVVGYGRWP TYLRDDEATA EDQPTQPDVA TCRFYTLDSI KWEKGSVGWW WKFPEALSDM GLFGQNMQY HYLGRAGYTI HVQCNASKFH QGCLLVVCVP EAEMGGAVVG QAFSATAMAN GDKAYEFTSA TQSDQTKVQT A IHNAGMGV ...String:
SDRVRSITLG NSTITTQECA NVVVGYGRWP TYLRDDEATA EDQPTQPDVA TCRFYTLDSI KWEKGSVGWW WKFPEALSDM GLFGQNMQY HYLGRAGYTI HVQCNASKFH QGCLLVVCVP EAEMGGAVVG QAFSATAMAN GDKAYEFTSA TQSDQTKVQT A IHNAGMGV GVGNLTIYPH QWINLRTNNS ATIVMPYINS VPMDNMFRHY NFTLMVIPFV KLDYADTAST YVPITVTVAP MC AEYNGLR LAQA

UniProtKB: Genome polyprotein

-
Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human coxsackievirus A9 (strain Griggs) / Strain: Griggs / Tissue: kidney
Molecular weightTheoretical: 26.335072 KDa
SequenceString: GLPTMNTPGS TQFLTSDDFQ SPCALPQFDV TPSMNIPGEV KNLMEIAEVD SVVPVNNVQD TTDQMEMFRI PVTINAPLQQ QVFGLRLQP GLDSVFKHTL LGEILNYYAH WSGSMKLTFV FCGSAMATGK FLIAYSPPGA NPPKTRKDAM LGTHIIWDIG L QSSCVLCV ...String:
GLPTMNTPGS TQFLTSDDFQ SPCALPQFDV TPSMNIPGEV KNLMEIAEVD SVVPVNNVQD TTDQMEMFRI PVTINAPLQQ QVFGLRLQP GLDSVFKHTL LGEILNYYAH WSGSMKLTFV FCGSAMATGK FLIAYSPPGA NPPKTRKDAM LGTHIIWDIG L QSSCVLCV PWISQTHYRL VQQDEYTSAG YVTCWYQTGM IVPPGTPNSS SIMCFASACN DFSVRMLRDT PFISQDNKLQ

UniProtKB: Genome polyprotein

-
Macromolecule #4: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human coxsackievirus A9 (strain Griggs) / Strain: Griggs / Tissue: kidney
Molecular weightTheoretical: 7.352039 KDa
SequenceString:
GAQVSTQKTG AHETSLSAAG NSIIHYTNIN YYKDAASNSA NRQDFTQDPS KFTEPVKDVM IKSLPALN

UniProtKB: Genome polyprotein

-
Macromolecule #5: 4-[(4-methylpiperazin-1-yl)methyl]-N-[[4-(trifluoromethyl)phenyl]...

MacromoleculeName: 4-[(4-methylpiperazin-1-yl)methyl]-N-[[4-(trifluoromethyl)phenyl]methyl]aniline
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1H8J
Molecular weightTheoretical: 363.42 Da

-
Macromolecule #6: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.2 / Details: PBS containing 2 mM MgCl2 and 5% DMSO.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295.15 K / Instrument: LEICA EM GP
Details: Sample was incubated for 15 s on the grid before blotted from the front for 1.5 s..
DetailsCompound 14 (CL275) was solubilized in DMSO and diluted to the final concentration in PBS + 2 mM MgCl2. Purified Coxsackievirus A9 was incubated with compound 14 (CL275) for 1h at 37C after which the sample was vitrified on a semi-automatic plunger Leica EM GP on copper Quantifoil R1.2/1.3 grids with thin carbon film and 300 mesh. This sample was monodisperse.

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 93.15 K / Max: 103.15 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 1496 pixel / Digitization - Dimensions - Height: 1496 pixel / Number grids imaged: 1 / Number real images: 567 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 0.7000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 16479
Startup modelType of model: OTHER
Details: Initial model was generated in cryoSPARC utilising Ab Initio model protocol.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.0)
Software - details: Non-uniform refinement job in cryoSPARC was used for final reconstruction angle assignment
Number images used: 16479
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
Software - details: Protocol for Ab Initio implemented in cryoSPARC was used for model creation
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.2.0)
Software - details: Heterogeneous refinement implemented in cryoSPARC was used for 3D classification
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

8at5


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementOverall B value: 95.8
Output model

PDB-9exi:
Coxsackievirus A9 bound with compound 14 (CL275)

+
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