[English] 日本語
Yorodumi
- EMDB-70751: Cowpea chlorotic mottle virus in contracted state 700 ms after pH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70751
TitleCowpea chlorotic mottle virus in contracted state 700 ms after pH shift triggered using Mix-it-up
Map data
Sample
  • Virus: Cowpea chlorotic mottle virus
    • Protein or peptide: Cowpea chlorotic mottle virus capsid
Keywordscowpea chlorotic mottle virus / plant / VIRUS
Biological speciesCowpea chlorotic mottle virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsAlexandrescu L / Lander GC
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1F31NS136003-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM154216 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143805 United States
CitationJournal: To Be Published
Title: "Mix-it-up": Accessible time-resolved cryo-EM on the millisecond timescale
Authors: Alexandrescu L / Lander GC
History
DepositionMay 20, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70751.png

Downloads & links

-
Map

FileDownload / File: emd_70751.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 560 pix.
= 526.4 Å		0.94 Å/pix.
x 560 pix.
= 526.4 Å		0.94 Å/pix.
x 560 pix.
= 526.4 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: 0.0812
Minimum - Maximum-0.12784834 - 0.24476725
Average (Standard dev.)0.00004346152 (±0.012928108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 526.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_70751_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_70751_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_70751_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_70751_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cowpea chlorotic mottle virus

EntireName: Cowpea chlorotic mottle virus
Components
  • Virus: Cowpea chlorotic mottle virus
    • Protein or peptide: Cowpea chlorotic mottle virus capsid

-
Supramolecule #1: Cowpea chlorotic mottle virus

SupramoleculeName: Cowpea chlorotic mottle virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12303 / Sci species name: Cowpea chlorotic mottle virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Vigna unguiculata subsp. unguiculata / Strain: No. 5
Molecular weightTheoretical: 3.8 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 290.0 Å / T number (triangulation number): 3

-
Macromolecule #1: Cowpea chlorotic mottle virus capsid

MacromoleculeName: Cowpea chlorotic mottle virus capsid / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Cowpea chlorotic mottle virus / Strain: No. 5
SequenceString:
MSTVGTGKLT RAQRRAAARK NKRNTRVVQP VIVEPIASGQ GKAIKAWTGY SVSKWTASCA AAEAKVTSAI TISLPNELSS ERNKQLKVGR VLLWLGLLPS VSGTVKSCVT ETQTTAAASF QVALAVADNS KDVVAAMYPE AFKGITLEQL TADLTIYLYS SAALTEGDVI VHLEVEHVRP TFDDSFTPVY

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration20 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Trisaminomethane
50.0 mMNaClSodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acid

Details: Sprayed with low pH buffer: 0.1M NaOAc, 1mM EDTA, pH 3.6
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 14 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 23.998 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 69 % / Chamber temperature: 296 K
Details: Vitrification performed at ambient humidity and room temperature using specialized "Mix-it-Up" electrospray device.

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 70.0 K / Max: 77.0 K
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3050 / Average exposure time: 4.08 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated defocus max: 3.9410000000000003 µm / Calibrated defocus min: 0.1 µm / Calibrated magnification: 148936 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 68342
CTF correctionSoftware - Name: cryoSPARC (ver. v4.6.2) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Number images used: 6889
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
Final 3D classificationNumber classes: 50 / Avg.num./class: 1164 / Software - Name: cryoSPARC (ver. v4.6.2)
FSC plot (resolution estimation)

+
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