[English] 日本語
Yorodumi
- EMDB-28238: Bacteriophage HRP29 Procapsid Icosohedral Reconstruction -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28238
TitleBacteriophage HRP29 Procapsid Icosohedral Reconstruction
Map data
SampleShigella phage HRP29 != Shigella phage Buco

Shigella phage HRP29

  • Virus: Shigella phage Buco (virus)
    • Protein or peptide: Gp37
KeywordsHRP29 / VIRUS
Function / homologyPutative capsid protein
Function and homology information
Biological speciesShigella phage Buco (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSubramanian S / Bergland Drarvik SM / Parent KN
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
National Science Foundation (NSF, United States)1750125 United States
CitationJournal: To Be Published
Title: Structure of Shigella bacteriophage HRP29
Authors: Subramanian S / Bergland Drarvik SM / Parent KN
History
DepositionSep 26, 2022-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28238.png

Downloads & links

-
Map

FileDownload / File: emd_28238.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 700 pix.
= 924. Å		1.32 Å/pix.
x 700 pix.
= 924. Å		1.32 Å/pix.
x 700 pix.
= 924. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.020515926 - 0.05800736
Average (Standard dev.)0.00035002193 (±0.0023470246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-349-349-349
Dimensions700700700
Spacing700700700
CellA=B=C: 924.00006 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_28238_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_28238_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_28238_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Shigella phage HRP29

EntireName: Shigella phage HRP29
Components
  • Virus: Shigella phage Buco (virus)
    • Protein or peptide: Gp37

-
Supramolecule #1: Shigella phage Buco

SupramoleculeName: Shigella phage Buco / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2530183 / Sci species name: Shigella phage Buco / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Shigella flexneri Y (bacteria)

-
Macromolecule #1: Gp37

MacromoleculeName: Gp37 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Buco (virus)
Molecular weightTheoretical: 36.911305 KDa
SequenceString: MANTDYAGNL TRPHWGGAAS DVDIHLEVYQ NEVDTRFQYQ AMFLGLSSQR SVADRSNTYR IDRLNTSSVK GRTSGVALEP TPVRNDKML IVVDTVLYIR NPIDYQDDWT APDFLTEMGQ NNGSEFAEVF DQAHLIQLIK GRSWVAPAHL KPAFSDGIEI E ATIDSDVT ...String:
MANTDYAGNL TRPHWGGAAS DVDIHLEVYQ NEVDTRFQYQ AMFLGLSSQR SVADRSNTYR IDRLNTSSVK GRTSGVALEP TPVRNDKML IVVDTVLYIR NPIDYQDDWT APDFLTEMGQ NNGSEFAEVF DQAHLIQLIK GRSWVAPAHL KPAFSDGIEI E ATIDSDVT TQAGMEANAI AINQAHKAGI DELIKRKVPL NDMITLVSTE IYSLLLEHPK LFNKDWGDAN ANGYKERRAV LM NGIPVVE CTEFPDAGTH PLGSAYTVTA DDAKCRMVTF SKSRTLVTVE AKPFTSRIWD DEQNFANVLD CYAMYQVGER RPD TAAVVK FNEAP

UniProtKB: Putative capsid protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
10.0 mMtris(hydroxymethyl)aminomethane
10.0 mMmagnesium chlorideMgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 38.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 60962
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
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