[English] 日本語
- EMDB-30139: Mature Phage Capsid -

Open data

ID or keywords:


Basic information

Database: EMDB / ID: EMD-30139
TitleMature Phage Capsid
Map data
SampleMature Phage Capsid
Biological speciesEscherichia phage T7 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen WY
Funding support1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
CitationJournal: Protein Cell / Year: 2020
Title: Structural changes of a bacteriophage upon DNA packaging and maturation.
Authors: Wenyuan Chen / Hao Xiao / Xurong Wang / Shuanglin Song / Zhen Han / Xiaowu Li / Fan Yang / Li Wang / Jingdong Song / Hongrong Liu / Lingpeng Cheng /
DepositionMar 20, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing site: PDBj / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_30139.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 540 pix.
= 685.8 Å
1.27 Å/pix.
x 540 pix.
= 685.8 Å
1.27 Å/pix.
x 540 pix.
= 685.8 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Contour LevelBy AUTHOR: 20.0 / Movie #1: 15
Minimum - Maximum-40.295258 - 90.283356
Average (Standard dev.)-0.104675695 (±8.459662)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 685.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z540540540
origin x/y/z0.0000.0000.000
length x/y/z685.800685.800685.800
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS-270-270-270
D min/max/mean-40.29590.283-0.105

Supplemental data

Sample components

Entire Mature Phage Capsid

EntireName: Mature Phage Capsid / Number of components: 1

Component #1: protein, Mature Phage Capsid

ProteinName: Mature Phage Capsid / Recombinant expression: No
SourceSpecies: Escherichia phage T7 (bacteriophage)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: NITROGEN

Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 24 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 58690
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

About Yorodumi


Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more


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.

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