[English] 日本語
Yorodumi
- EMDB-72122: MS2 bacteriophage coat protein after reassembly as a nanocrate (M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72122
TitleMS2 bacteriophage coat protein after reassembly as a nanocrate (MS2nc) with no cargo and with waters modeled
Map dataSharpened map, output from CryoSPARC non-uniform refinement.
Sample
  • Complex: Escherichia phage MS2 capsid protein
    • Protein or peptide: Capsid protein
  • Ligand: water
KeywordsBacteriophage / VLP / MS2 / nanocrate / VIRUS
Function / homology
Function and homology information


negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
Biological speciesEscherichia phage MS2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.74 Å
AuthorsZimanyi CM / Bobe D / Jenkins MC / Kopylov M
Funding support United States, 3 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI148382 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA247484 United States
CitationJournal: To Be Published
Title: Overcoming air-water interface-induced artifacts in Cryo-EM with protein nanocrates
Authors: Jenkins MC / Bobe D / Johnston JD / Cheung J / Karasawa A / Zimanyi CM / Dermanci O / Finn MG / de Marco A / Kopylov M
History
DepositionAug 13, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72122.png

Downloads & links

-
Map

FileDownload / File: emd_72122.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map, output from CryoSPARC non-uniform refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 397.92 Å		0.83 Å/pix.
x 480 pix.
= 397.92 Å		0.83 Å/pix.
x 480 pix.
= 397.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44
Minimum - Maximum-0.66447973 - 2.2656622
Average (Standard dev.)0.014789989 (±0.10270529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 397.91998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_72122_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map, output from CryoSPARC non-uniform refinement.

Fileemd_72122_additional_1.map
AnnotationUnsharpened map, output from CryoSPARC non-uniform refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unsharpened half map, output from CryoSPARC non-uniform refinement.

Fileemd_72122_half_map_1.map
AnnotationUnsharpened half map, output from CryoSPARC non-uniform refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unsharpened half map, output from CryoSPARC non-uniform refinement.

Fileemd_72122_half_map_2.map
AnnotationUnsharpened half map, output from CryoSPARC non-uniform refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia phage MS2 capsid protein

EntireName: Escherichia phage MS2 capsid protein
Components
  • Complex: Escherichia phage MS2 capsid protein
    • Protein or peptide: Capsid protein
  • Ligand: water

-
Supramolecule #1: Escherichia phage MS2 capsid protein

SupramoleculeName: Escherichia phage MS2 capsid protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Reassembled as a nanocrate with no cargo after disassembly and RNA removal.
Source (natural)Organism: Escherichia phage MS2 (virus)

-
Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage MS2 (virus)
Molecular weightTheoretical: 13.738464 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ASNFTQFVLV DNGGTGDVTV APSNFANGVA EWISSNSRSQ AYKVTCSVRQ SSAQNRKYTI KVEVPKVATQ TVGGVELPVA AWRSYLNME LTIPIFATNS DCELIVKAMQ GLLKDGNPIP SAIAANSGIY

UniProtKB: Capsid protein

-
Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 228 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8.5 / Details: 100 mM Tris-HCl [pH 8.5], 80 mM KCl, 10 mM MgCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2860 / Average exposure time: 1.25 sec. / Average electron dose: 54.58 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 348343
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 1.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 239460
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

2izm


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9q1b:
MS2 bacteriophage coat protein after reassembly as a nanocrate (MS2nc) with no cargo and with waters modeled

+
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