[English] 日本語
Yorodumi
- EMDB-68036: Cryo-EM structure of portal-adaptor of bacteriophage phi92 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-68036
TitleCryo-EM structure of portal-adaptor of bacteriophage phi92
Map data
Sample
  • Complex: Escherichia phage phi92
    • Protein or peptide: Phi92_gp120
    • Protein or peptide: Phi92_gp126
Keywordsportal adaptor / VIRAL PROTEIN
Function / homology: / Bacteriophage PhiTE adapter protein / Protein of unknown function DUF935 / Portal protein of Mu bacteriophage / Phi92_gp126 / Phi92_gp120
Function and homology information
Biological speciesEscherichia phage phi92 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen Y / Liu HR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: To Be Published
Title: Cryo-EM structure of portal-adaptor of bacteriophage phi92
Authors: Chen Y / Liu HR
History
DepositionDec 31, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_68036.png

Downloads & links

-
Map

FileDownload / File: emd_68036.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.1
Minimum - Maximum-4.9570103 - 9.341709
Average (Standard dev.)-0.00042120682 (±0.50950706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_68036_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_68036_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia phage phi92

EntireName: Escherichia phage phi92 (virus)
Components
  • Complex: Escherichia phage phi92
    • Protein or peptide: Phi92_gp120
    • Protein or peptide: Phi92_gp126

-
Supramolecule #1: Escherichia phage phi92

SupramoleculeName: Escherichia phage phi92 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage phi92 (virus)

-
Macromolecule #1: Phi92_gp120

MacromoleculeName: Phi92_gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 58.075262 KDa
SequenceString: MSTGKRKYTK RSDYWNKGST EKAALSPTQS ATKEKNLVLS PEIGTIGLNS IKAFTNFMQP YETRFPENIR TYKEMGEDPD VATALDATY IFVDRAFFDF KIKYNVSSAK SRRAAKFVDY TLRNMNAPLR QYVRSLLTYK QFGFAFAEKV YELDEDPKSP Y FGYYRLVK ...String:
MSTGKRKYTK RSDYWNKGST EKAALSPTQS ATKEKNLVLS PEIGTIGLNS IKAFTNFMQP YETRFPENIR TYKEMGEDPD VATALDATY IFVDRAFFDF KIKYNVSSAK SRRAAKFVDY TLRNMNAPLR QYVRSLLTYK QFGFAFAEKV YELDEDPKSP Y FGYYRLVK LAFRPQDTID LAQPFTYSDD GRTILTVNQN ITNGMVSPGT NATLIGRKEI PMEKVIYVGS NITENNPLGV SP LLAVYRS WREKSLIQEY EVVGVSKDLG GMPVLMVPSD ILNRASLNPS GDEAQSLRVL QANIANLHAG EQSYMVLPSD VYE GTVMRQ YDLVFQGVEG SGKQFDTQAL IKQRKLDIYN RFGAGVLIMG DGEGGSYSLS DNKQTLLSHF IERDVDIITE ALNT QVIPQ LLRLNGIFLS QEDMPKFVSD DIGDPDIEVN AKAIQQIVAA GAIPLTPEVI NEFFERLGFN YRIPDDIVAD PDKFQ EFLE TFMPDKTSRS GDGLAAGAGN GTSTSPAALD TSAANLAN

UniProtKB: Phi92_gp120

-
Macromolecule #2: Phi92_gp126

MacromoleculeName: Phi92_gp126 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 20.171738 KDa
SequenceString:
MLIASDLVPM IRILVFNPSQ ETLPDAMIEQ IIQTWIDVLG NDDANKCAVL WNSLISVLEY LWNTDVLNHN TQTGGALSRK EKVGEVQVE VTFGTGQTEY ISPWENIYKG YLDGDMMIPG CTSGRGVTSK VLVGGVDARE IDRVNSDPNS VNGLGGVGSV D RHTRNIKY ARNYGPIGYY RRDK

UniProtKB: Phi92_gp126

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 32000
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

+
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