[English] 日本語
Yorodumi
- PDB-6qzf: The cryo-EM structure of the collar complex and tail axis in geno... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qzf
TitleThe cryo-EM structure of the collar complex and tail axis in genome emptied bacteriophage phi29
Components
  • Portal protein
  • Pre-neck appendage protein
  • Proximal tail tube connector protein
KeywordsVIRUS / bacteriophage / phi29 / genome emptied virion
Function / homology
Function and homology information


virus tail, tube / viral portal complex / viral procapsid / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell / RNA binding ...virus tail, tube / viral portal complex / viral procapsid / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Peptidase G2, IMC autoproteolytic cleavage domain / Peptidase_G2, IMC autoproteolytic cleavage domain / Portal protein Gp10 / Portal protein Gp10 superfamily / Phage Connector (GP10) / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Portal protein / Pre-neck appendage protein / Proximal tail tube connector protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsXu, J. / Wang, D. / Gui, M. / Xiang, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501100 China
Ministry of Science and Technology (China)2015CB910102 China
National Natural Science Foundation of China31470721 China
CitationJournal: Nat Commun / Year: 2019
Title: Structural assembly of the tailed bacteriophage ϕ29.
Authors: Jingwei Xu / Dianhong Wang / Miao Gui / Ye Xiang /
Abstract: The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile ...The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile tail. Here, we report the near-atomic structures of the ϕ29 pre-genome packaging head (prohead), the mature virion and the genome-emptied virion. Structural comparisons suggest local rotation or oscillation of the head-tail connector upon DNA packaging and release. Termination of the DNA packaging occurs through pressure-dependent correlative positional and conformational changes in the connector. The funnel-shaped tail lower collar attaches the expanded narrow end of the connector and has a 180-Å long, 24-strand β barrel narrow stem tube that undergoes conformational changes upon genome release. The appendages form an interlocked assembly attaching the tail around the collar. The membrane active long loops at the distal end of the tail knob exit during the late stage of infection and form the cone-shaped tip of a largely hydrophobic helix barrel, prepared for membrane penetration.
History
DepositionMar 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Structure summary / Category: em_admin / pdbx_database_proc / struct
Item: _em_admin.last_update / _em_admin.title / _struct.title
Revision 1.2Oct 30, 2019Group: Author supporting evidence / Data collection / Database references
Category: em_image_scans / em_single_particle_entity / pdbx_database_related
Item: _pdbx_database_related.content_type
Revision 1.3May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-4685
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4685
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0a: Portal protein
0b: Portal protein
0c: Portal protein
0d: Portal protein
0e: Portal protein
0f: Portal protein
0g: Portal protein
0h: Portal protein
0i: Portal protein
0j: Portal protein
0k: Portal protein
0l: Portal protein
0A: Proximal tail tube connector protein
0B: Proximal tail tube connector protein
0C: Proximal tail tube connector protein
0D: Proximal tail tube connector protein
0E: Proximal tail tube connector protein
0F: Proximal tail tube connector protein
0G: Proximal tail tube connector protein
0H: Proximal tail tube connector protein
0I: Proximal tail tube connector protein
0J: Proximal tail tube connector protein
0K: Proximal tail tube connector protein
0L: Proximal tail tube connector protein
A: Pre-neck appendage protein
B: Pre-neck appendage protein
C: Pre-neck appendage protein
D: Pre-neck appendage protein
E: Pre-neck appendage protein
F: Pre-neck appendage protein
G: Pre-neck appendage protein
H: Pre-neck appendage protein
I: Pre-neck appendage protein
J: Pre-neck appendage protein
K: Pre-neck appendage protein
L: Pre-neck appendage protein
M: Pre-neck appendage protein
N: Pre-neck appendage protein
O: Pre-neck appendage protein
P: Pre-neck appendage protein
Q: Pre-neck appendage protein
R: Pre-neck appendage protein
S: Pre-neck appendage protein
T: Pre-neck appendage protein
U: Pre-neck appendage protein
V: Pre-neck appendage protein
W: Pre-neck appendage protein
X: Pre-neck appendage protein
Y: Pre-neck appendage protein
Z: Pre-neck appendage protein
a: Pre-neck appendage protein
b: Pre-neck appendage protein
c: Pre-neck appendage protein
d: Pre-neck appendage protein
e: Pre-neck appendage protein
f: Pre-neck appendage protein
g: Pre-neck appendage protein
h: Pre-neck appendage protein
i: Pre-neck appendage protein
j: Pre-neck appendage protein


Theoretical massNumber of molelcules
Total (without water)4,156,04360
Polymers4,156,04360
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Portal protein / Connector protein / Gene product 10 / gp10 / Gene product 19 / gp19 / Head-to-tail connector / ...Connector protein / Gene product 10 / gp10 / Gene product 19 / gp19 / Head-to-tail connector / Probable portal protein / Protein p10 / Upper collar protein


Mass: 35917.293 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacillus phage phi29 (virus) / References: UniProt: P04332
#2: Protein
Proximal tail tube connector protein / Gene product 11 / gp11 / Lower collar protein / Protein p11


Mass: 33839.086 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Details: the residues from 170 to 191 are assigned poly-alanine due to poor quality of map
Source: (natural) Bacillus phage phi29 (virus) / References: UniProt: P68930
#3: Protein ...
Pre-neck appendage protein / Gene product 12 / gp12 / NP1 / Protein p12


Mass: 92193.523 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Bacillus phage phi29 (virus) / References: UniProt: P20345

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Bacillus phage phi29 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacillus phage phi29 (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: PRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31478 / Symmetry type: POINT

+
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