[English] 日本語
Yorodumi
- PDB-8u11: In situ cryo-EM structure of bacteriophage P22 gp1:gp5:gp4: gp10:... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u11
TitleIn situ cryo-EM structure of bacteriophage P22 gp1:gp5:gp4: gp10: gp9 N-term complex in conformation 2 at 3.1A resolution
Components
  • Major capsid protein
  • Packaged DNA stabilization protein gp10
  • Peptidoglycan hydrolase gp4
  • Portal protein
  • Tail spike protein
KeywordsVIRAL PROTEIN / phage / bacteriophage / tail spike protein / TSP / gene product 9 (gp9) / Packaged DNA stabilization protein / gene product 10 (gp10) / STRUCTURAL PROTEIN / head-to-tail protein / gene product 4 (gp4) / Tail hub protein / gene product (1) / Portal protein / Coat protein / Major capsid protein / gene product 5 (gp5)
Function / homology
Function and homology information


viral DNA genome packaging, headful / endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / viral procapsid / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / viral procapsid maturation ...viral DNA genome packaging, headful / endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / viral procapsid / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / viral procapsid maturation / viral DNA genome packaging / virus tail / symbiont entry into host / T=7 icosahedral viral capsid / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / virion assembly / metabolic process / viral capsid / hydrolase activity / virion attachment to host cell / identical protein binding
Similarity search - Function
Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Tail accessory factor GP4 / Phage P22-like portal protein / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Major capsid protein Gp5 / P22 coat protein - gene protein 5 / P22 tailspike C-terminal domain ...Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Tail accessory factor GP4 / Phage P22-like portal protein / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Major capsid protein Gp5 / P22 coat protein - gene protein 5 / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Tail spike protein / Portal protein / Peptidoglycan hydrolase gp4 / Major capsid protein / Packaged DNA stabilization protein gp10
Similarity search - Component
Biological speciesSalmonella phage P22 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsIglesias, S. / Feng-Hou, C. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140733 United States
CitationJournal: J Mol Biol / Year: 2023
Title: Molecular Architecture of Salmonella Typhimurium Virus P22 Genome Ejection Machinery.
Authors: Stephano M Iglesias / Ravi K Lokareddy / Ruoyu Yang / Fenglin Li / Daniel P Yeggoni / Chun-Feng David Hou / Makayla N Leroux / Juliana R Cortines / Justin C Leavitt / Mary Bird / Sherwood R ...Authors: Stephano M Iglesias / Ravi K Lokareddy / Ruoyu Yang / Fenglin Li / Daniel P Yeggoni / Chun-Feng David Hou / Makayla N Leroux / Juliana R Cortines / Justin C Leavitt / Mary Bird / Sherwood R Casjens / Simon White / Carolyn M Teschke / Gino Cingolani /
Abstract: Bacteriophage P22 is a prototypical member of the Podoviridae superfamily. Since its discovery in 1952, P22 has become a paradigm for phage transduction and a model for icosahedral viral capsid ...Bacteriophage P22 is a prototypical member of the Podoviridae superfamily. Since its discovery in 1952, P22 has become a paradigm for phage transduction and a model for icosahedral viral capsid assembly. Here, we describe the complete architecture of the P22 tail apparatus (gp1, gp4, gp10, gp9, and gp26) and the potential location and organization of P22 ejection proteins (gp7, gp20, and gp16), determined using cryo-EM localized reconstruction, genetic knockouts, and biochemical analysis. We found that the tail apparatus exists in two equivalent conformations, rotated by ∼6° relative to the capsid. Portal protomers make unique contacts with coat subunits in both conformations, explaining the 12:5 symmetry mismatch. The tail assembles around the hexameric tail hub (gp10), which folds into an interrupted β-propeller characterized by an apical insertion domain. The tail hub connects proximally to the dodecameric portal protein and head-to-tail adapter (gp4), distally to the trimeric tail needle (gp26), and laterally to six trimeric tailspikes (gp9) that attach asymmetrically to gp10 insertion domain. Cryo-EM analysis of P22 mutants lacking the ejection proteins gp7 or gp20 and biochemical analysis of purified recombinant proteins suggest that gp7 and gp20 form a molecular complex associated with the tail apparatus via the portal protein barrel. We identified a putative signal transduction pathway from the tailspike to the tail needle, mediated by three flexible loops in the tail hub, that explains how lipopolysaccharide (LPS) is sufficient to trigger the ejection of the P22 DNA in vitro.
History
DepositionAug 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Packaged DNA stabilization protein gp10
2: Packaged DNA stabilization protein gp10
3: Packaged DNA stabilization protein gp10
4: Packaged DNA stabilization protein gp10
5: Packaged DNA stabilization protein gp10
6: Packaged DNA stabilization protein gp10
7: Tail spike protein
8: Tail spike protein
9: Tail spike protein
10: Tail spike protein
11: Tail spike protein
12: Tail spike protein
13: Tail spike protein
14: Tail spike protein
15: Tail spike protein
16: Tail spike protein
17: Tail spike protein
18: Tail spike protein
19: Tail spike protein
20: Tail spike protein
21: Tail spike protein
22: Tail spike protein
23: Tail spike protein
24: Tail spike protein
a: Portal protein
y: Peptidoglycan hydrolase gp4
b: Portal protein
m: Peptidoglycan hydrolase gp4
c: Portal protein
n: Peptidoglycan hydrolase gp4
d: Portal protein
o: Peptidoglycan hydrolase gp4
e: Portal protein
p: Peptidoglycan hydrolase gp4
l: Portal protein
q: Peptidoglycan hydrolase gp4
f: Portal protein
r: Peptidoglycan hydrolase gp4
k: Portal protein
s: Peptidoglycan hydrolase gp4
i: Portal protein
t: Peptidoglycan hydrolase gp4
j: Portal protein
u: Peptidoglycan hydrolase gp4
h: Portal protein
v: Peptidoglycan hydrolase gp4
g: Portal protein
x: Peptidoglycan hydrolase gp4
E: Major capsid protein
C: Major capsid protein
A: Major capsid protein
G: Major capsid protein
I: Major capsid protein
D: Major capsid protein
B: Major capsid protein
F: Major capsid protein
H: Major capsid protein
J: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)3,288,14458
Polymers3,288,14458
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Packaged DNA stabilization protein gp10


Mass: 52512.020 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26749
#2: Protein
Tail spike protein


Mass: 71923.523 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P12528
#3: Protein
Portal protein


Mass: 82829.375 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26744
#4: Protein
Peptidoglycan hydrolase gp4


Mass: 18044.959 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26746
#5: Protein
Major capsid protein


Mass: 46795.613 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26747

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Salmonella phage P22 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella phage P22 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Salmonella enterica
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 29000 X / Calibrated magnification: 29000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2100 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.08 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
Image scansWidth: 11520 / Height: 8184

-
Processing

EM software
IDNameVersionCategory
2PHENIX1.20.1_4487:model refinement
13RELION3.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17944 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 55.42 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0059141264
ELECTRON MICROSCOPYf_angle_d0.6276191741
ELECTRON MICROSCOPYf_chiral_restr0.048121178
ELECTRON MICROSCOPYf_plane_restr0.004925189
ELECTRON MICROSCOPYf_dihedral_angle_d4.9319221

+
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