[English] 日本語
Yorodumi
- PDB-6psk: Crystal structure of the complex between periplasmic domains of a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6psk
TitleCrystal structure of the complex between periplasmic domains of antiholin RI and holin T from T4 phage, in P6522
Components
  • Antiholin
  • Holin
KeywordsVIRAL PROTEIN / phage / lysis inhibition
Function / homology
Function and homology information


: / host cell periplasmic space / pore-forming activity / cytolysis / molecular function inhibitor activity / viral release from host cell by cytolysis / killing of cells of another organism / host cell plasma membrane / DNA binding / membrane
Similarity search - Function
Bacteriophage T4, GpT, holin / Bacteriophage T holin / Antiholin T4 type
Similarity search - Domain/homology
Holin / Antiholin / Holin / Antiholin
Similarity search - Component
Biological speciesEscherichia phage ECML-134 (virus)
Escherichia phage vB_EcoM_NBG2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKuznetsov, V.B. / Krieger, I.V. / Sacchettini, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationA-0015 United States
CitationJournal: J Mol Biol / Year: 2020
Title: The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition.
Authors: Inna V Krieger / Vladimir Kuznetsov / Jeng-Yih Chang / Junjie Zhang / Samir H Moussa / Ryland F Young / James C Sacchettini /
Abstract: Optimal phage propagation depends on the regulation of the lysis of the infected host cell. In T4 phage infection, lysis occurs when the holin protein (T) forms lesions in the host membrane. However, ...Optimal phage propagation depends on the regulation of the lysis of the infected host cell. In T4 phage infection, lysis occurs when the holin protein (T) forms lesions in the host membrane. However, the lethal function of T can be blocked by an antiholin (RI) during lysis inhibition (LIN). LIN sets if the infected cell undergoes superinfection, then the lysis is delayed until host/phage ratio becomes more favorable for the release of progeny. It has been thought that a signal derived from the superinfection is required to activate RI. Here we report structures that suggest a radically different model in which RI binds to T irrespective of superinfection, causing it to accumulate in a membrane as heterotetrameric 2RI-2T complex. Moreover, we show the complex binds non-specifically to DNA, suggesting that the gDNA from the superinfecting phage serves as the LIN signal and that stabilization of the complex by DNA binding is what defines LIN. Finally, we show that soluble domain of free RI crystallizes in a domain-swapped homotetramer, which likely works as a sink for RI molecules released from the RI-T complex to ensure efficient lysis. These results constitute the first structural basis and a new model not only for the historic LIN phenomenon but also for the temporal regulation of phage lysis in general.
History
DepositionJul 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: Antiholin
T: Holin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,96711
Polymers27,1862
Non-polymers7819
Water1,31573
1
T: Holin
hetero molecules

T: Holin
hetero molecules

R: Antiholin
hetero molecules

R: Antiholin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,93522
Polymers54,3724
Non-polymers1,56218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation5_555y,-x+y,z+1/61
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area8160 Å2
ΔGint-103 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.666, 120.666, 85.513
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11T-438-

HOH

21T-449-

HOH

-
Components

-
Protein , 2 types, 2 molecules RT

#1: Protein Antiholin


Mass: 9083.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage ECML-134 (virus) / Gene: ECML134_104 / Production host: Escherichia coli (E. coli) / References: UniProt: I7AU04, UniProt: P13304*PLUS
#2: Protein Holin /


Mass: 18102.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage vB_EcoM_NBG2 (virus) / Gene: vBEcoMNBG2_239 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U8QQK7, UniProt: P06808*PLUS

-
Non-polymers , 5 types, 82 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, and 1% PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.987 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→45 Å / Num. obs: 19177 / % possible obs: 100 % / Redundancy: 40.8 % / Biso Wilson estimate: 42.34 Å2 / Rsym value: 0.156 / Net I/av σ(I): 0.415 / Net I/σ(I): 16.17
Reflection shell
Resolution (Å)Num. unique obsRsym valueDiffraction-ID
2.2-2.37340.77951
2.23-2.2811661
2.28-2.328441
2.32-2.379961
2.37-2.429051
2.42-2.4810031
2.48-2.5510591
2.55-2.629431
2.62-2.79541
2.7-2.799691

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SAINTdata scaling
PDB_EXTRACT3.25data extraction
TRUNCATEdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→44.586 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.88
RfactorNum. reflection% reflection
Rfree0.2468 918 4.8 %
Rwork0.2127 --
obs0.2144 19136 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.43 Å2 / Biso mean: 44.6793 Å2 / Biso min: 27.09 Å2
Refinement stepCycle: final / Resolution: 2.2→44.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 46 73 1891
Biso mean--63.85 46.02 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091856
X-RAY DIFFRACTIONf_angle_d0.8932497
X-RAY DIFFRACTIONf_chiral_restr0.048254
X-RAY DIFFRACTIONf_plane_restr0.006316
X-RAY DIFFRACTIONf_dihedral_angle_d8.6111104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.3160.35681240.28732542
2.316-2.46110.2911280.27262551
2.4611-2.65110.31441210.25362560
2.6511-2.91780.32391440.24062548
2.9178-3.33990.28681340.22352601
3.3399-4.20750.2281290.19222630
4.2075-44.580.1941380.18772786

+
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