[English] 日本語
Yorodumi
- PDB-8qem: Neck channel of phage 812 after tail contraction (C1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qem
TitleNeck channel of phage 812 after tail contraction (C1)
Components
  • Channel DNA forward strand (63-MER)
  • Channel DNA reverse strand (63-MER)
  • Portal protein
  • Putative neck protein
KeywordsVIRUS / phage / neck / A-form DNA / connector
Function / homologyBacteriophage/Gene transfer agent portal protein / Phage portal protein / symbiont entry into host cell / DNA / DNA (> 10) / Portal protein / Neck protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsCienikova, Z. / Siborova, M. / Fuzik, T. / Plevka, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic Czech Republic
CitationJournal: To Be Published
Title: Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812
Authors: Cienikova, Z. / Novacek, J. / Siborova, M. / Popelarova, B. / Fuzik, T. / Benesik, M. / Bardy, P. / Plevka, P.
History
DepositionAug 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative neck protein
B: Putative neck protein
C: Putative neck protein
D: Putative neck protein
E: Putative neck protein
F: Putative neck protein
G: Putative neck protein
H: Putative neck protein
I: Putative neck protein
J: Putative neck protein
K: Putative neck protein
L: Putative neck protein
M: Portal protein
N: Portal protein
O: Portal protein
P: Portal protein
Q: Portal protein
R: Portal protein
S: Portal protein
T: Portal protein
U: Portal protein
V: Portal protein
W: Portal protein
X: Portal protein
Z: Channel DNA reverse strand (63-MER)
Y: Channel DNA forward strand (63-MER)


Theoretical massNumber of molelcules
Total (without water)1,218,99526
Polymers1,218,99526
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Putative neck protein


Mass: 34191.703 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTN6
#2: Protein
Portal protein


Mass: 64155.684 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A0A0U1WIV9
#3: DNA chain Channel DNA reverse strand (63-MER)


Mass: 19439.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420
#4: DNA chain Channel DNA forward strand (63-MER)


Mass: 19386.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Staphylococcus phage 812 / Type: VIRUS
Details: Purified phage virion was incubated in urea and LTA to induce tail contraction and genome ejection
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Staphylococcus aureus / Strain: CCM 8428
Virus shellDiameter: 1100 nm
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
210 mMsodium chlorideNaCl1
310 mMcalcium chlorideCaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7 sec. / Electron dose: 42 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15371
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansWidth: 4000 / Height: 4000 / Movie frames/image: 40

-
Processing

EM software
IDNameVersionCategory
1Gautomatch0.56particle selection
2SerialEMimage acquisition
4Gctf1.0.6CTF correction
7Coot0.9model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.19model refinement
Image processingDetails: Frame alignment and dose-weighting with MotionCor2, then contrast inversion and normalization
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 32222
Details: Particle selection using cross-correlation against capsid template
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13296 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation coefficient
Details: B-A-B-form dsDNA model was generated with Web 3DNA 2.0. Portal and neck dodecamers were sourced from models refined in C12 symmetry. All input models were fitted into the asymmetric map. ...Details: B-A-B-form dsDNA model was generated with Web 3DNA 2.0. Portal and neck dodecamers were sourced from models refined in C12 symmetry. All input models were fitted into the asymmetric map. Tunnel loops of the portal were extended into the asymmetric density.
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeInitial refinement model-IDSource nameTypeDetails
18Q7D

8q7d

8Q7D1PDBexperimental model
2Otherin silico modelWeb 3DNA 2.0
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00472818
ELECTRON MICROSCOPYf_angle_d0.68998735
ELECTRON MICROSCOPYf_dihedral_angle_d13.02310509
ELECTRON MICROSCOPYf_chiral_restr0.04510441
ELECTRON MICROSCOPYf_plane_restr0.00812510

+
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