[English] 日本語
Yorodumi
- EMDB-20956: Portal vertex structure of bacteriophage T4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20956
TitlePortal vertex structure of bacteriophage T4
Map datalow-pass filtered and B-factor sharpened map
Sample
  • Virus: Escherichia virus T4
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Portal protein
Keywordsportal protein assembly / gp20 / gp23 / portal vertex / VIRUS
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, contractile tail mechanism / T=13 icosahedral viral capsid / viral portal complex / viral genome packaging / viral release from host cell / viral capsid / host cell plasma membrane / membrane
Similarity search - Function
Portal protein Gp20 / Bacteriophage T4-like portal protein (Gp20) / Major capsid protein, Myoviridae / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like
Similarity search - Domain/homology
Major capsid protein / Portal protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus) / Escherichia virus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsFang Q / Fokine A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural morphing in a symmetry-mismatched viral vertex.
Authors: Qianglin Fang / Wei-Chun Tang / Pan Tao / Marthandan Mahalingam / Andrei Fokine / Michael G Rossmann / Venigalla B Rao /
Abstract: Large biological structures are assembled from smaller, often symmetric, sub-structures. However, asymmetry among sub-structures is fundamentally important for biological function. An extreme form of ...Large biological structures are assembled from smaller, often symmetric, sub-structures. However, asymmetry among sub-structures is fundamentally important for biological function. An extreme form of asymmetry, a 12-fold-symmetric dodecameric portal complex inserted into a 5-fold-symmetric capsid vertex, is found in numerous icosahedral viruses, including tailed bacteriophages, herpesviruses, and archaeal viruses. This vertex is critical for driving capsid assembly, DNA packaging, tail attachment, and genome ejection. Here, we report the near-atomic in situ structure of the symmetry-mismatched portal vertex from bacteriophage T4. Remarkably, the local structure of portal morphs to compensate for symmetry-mismatch, forming similar interactions in different capsid environments while maintaining strict symmetry in the rest of the structure. This creates a unique and unusually dynamic symmetry-mismatched vertex that is central to building an infectious virion.
History
DepositionNov 14, 2019-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6uzc
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6uzc
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20956.png

Downloads & links

-
Map

FileDownload / File: emd_20956.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlow-pass filtered and B-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 500 pix.
= 720. Å		1.44 Å/pix.
x 500 pix.
= 720. Å		1.44 Å/pix.
x 500 pix.
= 720. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-18.706944 - 30.373089
Average (Standard dev.)0.019396635 (±0.6027698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-250-250100
Dimensions500500500
Spacing500500500
CellA=B=C: 720.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.441.441.44
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z720.000720.000720.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS-250-250100
NC/NR/NS500500500
D min/max/mean-18.70730.3730.019

-
Supplemental data

-
Additional map: unfiltered map

Fileemd_20956_additional_1.map
Annotationunfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Supplemental map: emd 20956 additional 2.map

Fileemd_20956_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia virus T4

EntireName: Escherichia virus T4
Components
  • Virus: Escherichia virus T4
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Portal protein

-
Supramolecule #1: Escherichia virus T4

SupramoleculeName: Escherichia virus T4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10665 / Sci species name: Escherichia virus T4 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

-
Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 56.074242 KDa
SequenceString: MTIKTKAELL NKWKPLLEGE GLPEIANSKQ AIIAKIFENQ EKDFQTAPEY KDEKIAQAFG SFLTEAEIGG DHGYNATNIA AGQTSGAVT QIGPAVMGMV RRAIPNLIAF DICGVQPMNS PTGQVFALRA VYGKDPVAAG AKEAFHPMYG PDAMFSGQGA A KKFPALAA ...String:
MTIKTKAELL NKWKPLLEGE GLPEIANSKQ AIIAKIFENQ EKDFQTAPEY KDEKIAQAFG SFLTEAEIGG DHGYNATNIA AGQTSGAVT QIGPAVMGMV RRAIPNLIAF DICGVQPMNS PTGQVFALRA VYGKDPVAAG AKEAFHPMYG PDAMFSGQGA A KKFPALAA STQTTVGDIY THFFQETGTV YLQASVQVTI DAGATDAAKL DAEIKKQMEA GALVEIAEGM ATSIAELQEG FN GSTDNPW NEMGFRIDKQ VIEAKSRQLK AAYSIELAQD LRAVHGMDAD AELSGILATE IMLEINREVV DWINYSAQVG KSG MTLTPG SKAGVFDFQD PIDIRGARWA GESFKALLFQ IDKEAVEIAR QTGRGEGNFI IASRNVVNVL ASVDTGISYA AQGL ATGFS TDTTKSVFAG VLGGKYRVYI DQYAKQDYFT VGYKGPNEMD AGIYYAPYVA LTPLRGSDPK NFQPVMGFKT RYGIG INPF AESAAQAPAS RIQSGMPSIL NSLGKNAYFR RVYVKGI

UniProtKB: Major capsid protein

-
Macromolecule #2: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 61.117082 KDa
SequenceString: MKFNVLSLFA PWAKMDERNF KDQEKEDLVS ITAPKLDDGA REFEVSSNEA ASPYNAAFQT IFGSYEPGMK TTRELIDTYR NLMNNYEVD NAVSEIVSDA IVYEDDTEVV ALNLDKSKFS PKIKNMMLDE FSDVLNHLSF QRKGSDHFRR WYVDSRIFFH K IIDPKRPK ...String:
MKFNVLSLFA PWAKMDERNF KDQEKEDLVS ITAPKLDDGA REFEVSSNEA ASPYNAAFQT IFGSYEPGMK TTRELIDTYR NLMNNYEVD NAVSEIVSDA IVYEDDTEVV ALNLDKSKFS PKIKNMMLDE FSDVLNHLSF QRKGSDHFRR WYVDSRIFFH K IIDPKRPK EGIKELRRLD PRQVQYVREI ITETEAGTKI VKGYKEYFIY DTAHESYACD GRMYEAGTKI KIPKAAVVYA HS GLVDCCG KNIIGYLHRA VKPANQLKLL EDAVVIYRIT RAPDRRVWYV DTGNMPARKA AEHMQHVMNT MKNRVVYDAS TGK IKNQQH NMSMTEDYWL QRRDGKAVTE VDTLPGADNT GNMEDIRWFR QALYMALRVP LSRIPQDQQG GVMFDSGTSI TRDE LTFAK FIRELQHKFE EVFLDPLKTN LLLKGIITED EWNDEINNIK IEFHRDSYFA ELKEAEILER RINMLTMAEP FIGKY ISHR TAMKDILQMT DEEIEQEAKQ IEEESKEARF QDPDQEQEDF

UniProtKB: Portal protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 23.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53608
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6uzc:
Portal vertex structure of bacteriophage T4

+
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