[English] 日本語
Yorodumi
- EMDB-22931: The capsid of Myoviridae Phage XM1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22931
TitleThe capsid of Myoviridae Phage XM1
Map data
Sample
  • Virus: Vibrio phage XM1 (virus)
    • Protein or peptide: Minor capsid protein
    • Protein or peptide: Major capsid protein
KeywordsMyoviridae / Vibrio phage / Capsid / HK97 fold / VIRUS
Biological speciesVibrio phage XM1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang Z / Klose T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Biorxiv / Year: 2021
Title: Structure of Vibrio phage XM1, a simple contractile DNA injection machine
Authors: Wang Z / Fokine A / Guo X / Jiang W / Rossmann MG / Kuhn RJ / Luo ZH / Klose T
History
DepositionNov 3, 2020-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.37
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.37
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7kmx
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kmx
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22931.png

Downloads & links

-
Map

FileDownload / File: emd_22931.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 960 pix.
= 777.6 Å		0.81 Å/pix.
x 960 pix.
= 777.6 Å		0.81 Å/pix.
x 960 pix.
= 777.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.37 / Movie #1: 5.37
Minimum - Maximum-13.564842000000001 - 19.538278999999999
Average (Standard dev.)0.009352921 (±1.2176452)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-480-480-480
Dimensions960960960
Spacing960960960
CellA=B=C: 777.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z960960960
origin x/y/z0.0000.0000.000
length x/y/z777.600777.600777.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ640640640
MAP C/R/S123
start NC/NR/NS-480-480-480
NC/NR/NS960960960
D min/max/mean-13.56519.5380.009

-
Supplemental data

-
Sample components

-
Entire : Vibrio phage XM1

EntireName: Vibrio phage XM1 (virus)
Components
  • Virus: Vibrio phage XM1 (virus)
    • Protein or peptide: Minor capsid protein
    • Protein or peptide: Major capsid protein

-
Supramolecule #1: Vibrio phage XM1

SupramoleculeName: Vibrio phage XM1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2748688 / Sci species name: Vibrio phage XM1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Vibrio rotiferianus (bacteria)
Virus shellShell ID: 1 / Name: capsid / Diameter: 640.0 Å / T number (triangulation number): 7

-
Macromolecule #1: Minor capsid protein

MacromoleculeName: Minor capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 16.823863 KDa
SequenceString:
MAFNNAVLQE VSDLPAGEVI KASPHNVSAF EVFQNGLIEG RFVKFDAGSI DILDASATPT IAGIAKRKVT GEIGPGVYST SGIEIDQVA EVINFGFATV TVQDAAAPSK YDPVYAINLD SAEAGKATEN SGATGALAVA DCVFWEQKAA NVWLVRMNKF L

-
Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 35.512773 KDa
SequenceString: MKKDLKFIKS VYDLKSFSDK AAFAKKTFKD EGGIILARNL EHVSSEIFTQ EFAGLTFLQG GIVVNNEGGY ATSVTKLKLK AEGGFRESG NDTNTTGKIT LSGESDSIPV FTLEGESDWS EIELKQAELQ NVNLPSRYFE AHAELYNRKI DELGYLGQTR T DGTQKTLG ...String:
MKKDLKFIKS VYDLKSFSDK AAFAKKTFKD EGGIILARNL EHVSSEIFTQ EFAGLTFLQG GIVVNNEGGY ATSVTKLKLK AEGGFRESG NDTNTTGKIT LSGESDSIPV FTLEGESDWS EIELKQAELQ NVNLPSRYFE AHAELYNRKI DELGYLGQTR T DGTQKTLG LLNYGFVASG AGDTAANLSG DNLYQAIADL ITDQWAGVFN VETYKADRVV MPDTVYNICA KKILNSNGSE MS VLRALMT NFPTVTFGLT TKARDVGGTS RTTAYSSNRR AMQMRIPTPL NVSSVDQRGF KYYVESYFGV AGLDVIEDTA GRH LTGL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 50 mM Tris, pH 7.5, 100 mM NaCl, 8 mM MgSO4
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 19625
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7kmx:
The capsid of Myoviridae Phage XM1

+
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