[English] 日本語
Yorodumi
- PDB-4zv0: Structure of Tse6 in complex with Tsi6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zv0
TitleStructure of Tse6 in complex with Tsi6
Components
  • Tse6-binding/Tse6 immunity protein
  • antibacterial effector secreted protein (type VI secretion system)
KeywordsPROTEIN BINDING / T6SS effector-immunity pair
Function / homology
Function and homology information


protein secretion by the type VI secretion system / NAD+ glycohydrolase / toxin sequestering activity / NADP+ nucleosidase activity / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / membrane
Similarity search - Function
Tsi6 / Tsi6 / Bacterial toxin 46 / Bacterial toxin 46 / PAAR motif / PAAR motif
Similarity search - Domain/homology
IODIDE ION / NAD(P)(+) glycohydrolase toxin Tse6 / Immune protein Tsi6
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.401 Å
AuthorsWhitney, J.C. / Sawai, S. / Ralston, C. / Mougous, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI080609 United States
Defense Threat Reduction Agency (DTRA)HDTRA-1-13-014 United States
CitationJournal: Cell / Year: 2015
Title: An interbacterial NAD(P)(+) glycohydrolase toxin requires elongation factor Tu for delivery to target cells.
Authors: John C Whitney / Dennis Quentin / Shin Sawai / Michele LeRoux / Brittany N Harding / Hannah E Ledvina / Bao Q Tran / Howard Robinson / Young Ah Goo / David R Goodlett / Stefan Raunser / Joseph D Mougous /
Abstract: Type VI secretion (T6S) influences the composition of microbial communities by catalyzing the delivery of toxins between adjacent bacterial cells. Here, we demonstrate that a T6S integral membrane ...Type VI secretion (T6S) influences the composition of microbial communities by catalyzing the delivery of toxins between adjacent bacterial cells. Here, we demonstrate that a T6S integral membrane toxin from Pseudomonas aeruginosa, Tse6, acts on target cells by degrading the universally essential dinucleotides NAD(+) and NADP(+). Structural analyses of Tse6 show that it resembles mono-ADP-ribosyltransferase proteins, such as diphtheria toxin, with the exception of a unique loop that both excludes proteinaceous ADP-ribose acceptors and contributes to hydrolysis. We find that entry of Tse6 into target cells requires its binding to an essential housekeeping protein, translation elongation factor Tu (EF-Tu). These proteins participate in a larger assembly that additionally directs toxin export and provides chaperone activity. Visualization of this complex by electron microscopy defines the architecture of a toxin-loaded T6S apparatus and provides mechanistic insight into intercellular membrane protein delivery between bacteria.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: antibacterial effector secreted protein (type VI secretion system)
B: Tse6-binding/Tse6 immunity protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,29212
Polymers29,0232
Non-polymers1,26910
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-13 kcal/mol
Surface area11390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.209, 83.209, 83.758
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein antibacterial effector secreted protein (type VI secretion system)


Mass: 18282.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA0093 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: Q9I739
#2: Protein Tse6-binding/Tse6 immunity protein


Mass: 10740.220 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA0092 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: Q9I740
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350, 0.2M ammonium iodide

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 69121 / % possible obs: 99.9 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 33.5
Reflection shellResolution: 1.37→1.42 Å / Rmerge(I) obs: 0.617 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.401→37.261 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 15.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1643 2022 3.13 %
Rwork0.1465 --
obs0.1471 64549 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.401→37.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 10 366 2201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0221885
X-RAY DIFFRACTIONf_angle_d1.7132561
X-RAY DIFFRACTIONf_dihedral_angle_d13.567712
X-RAY DIFFRACTIONf_chiral_restr0.103279
X-RAY DIFFRACTIONf_plane_restr0.01339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4008-1.43590.22451430.19924443X-RAY DIFFRACTION100
1.4359-1.47470.18581400.18074453X-RAY DIFFRACTION100
1.4747-1.51810.19391460.16694443X-RAY DIFFRACTION100
1.5181-1.56710.16511470.15554439X-RAY DIFFRACTION100
1.5671-1.62310.19451430.15384456X-RAY DIFFRACTION100
1.6231-1.68810.16371430.14214456X-RAY DIFFRACTION100
1.6881-1.76490.16351420.14154470X-RAY DIFFRACTION100
1.7649-1.85790.18461470.144445X-RAY DIFFRACTION100
1.8579-1.97430.16511440.13374482X-RAY DIFFRACTION100
1.9743-2.12680.13671400.13184446X-RAY DIFFRACTION100
2.1268-2.34080.13831450.13364482X-RAY DIFFRACTION100
2.3408-2.67940.18031460.14024492X-RAY DIFFRACTION100
2.6794-3.37540.15721490.15274480X-RAY DIFFRACTION100
3.3754-37.27410.16121470.14864540X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.31540.3656-0.32696.2154-3.74124.3369-0.1428-0.14640.11210.44260.1960.1567-0.271-0.1404-0.06910.09050.0534-0.01130.1315-0.00780.101621.895935.172755.7475
20.8768-0.16570.35460.638-0.74131.20830.03590.0908-0.0258-0.0885-0.0725-0.05850.20410.26560.00150.09250.05080.00260.11230.00020.106219.759532.67637.8521
30.6843-0.5602-0.10970.4943-0.13672.20040.05350.17660.113-0.0308-0.1113-0.1836-0.10650.62380.04240.09050.02160.01210.26430.04370.149929.823534.806637.205
43.5451-2.3055-0.97851.62280.60020.49790.05720.6758-1.55910.1416-0.10570.70150.4633-0.2436-0.03330.32060.0011-0.01820.2752-0.02010.41089.373623.201343.7197
51.20450.1865-1.32851.8137-1.40262.54670.09310.29430.0051-0.1965-0.1672-0.1910.14750.25470.05380.07020.042-0.00140.19780.02490.118127.247336.594735.0809
60.991-0.1382-0.70121.13961.13684.64090.01870.0540.1224-0.00930.01130.1278-0.2085-0.1921-0.02060.07210.0103-0.00560.11420.02710.1315-1.699441.959638.9628
71.4633-0.2162-2.99770.63880.37156.7592-0.0526-0.0018-0.06260.05180.01190.05130.2027-0.15680.05390.0561-0.0133-0.01150.09940.00280.0922-1.205832.635441.5639
85.30180.1846-2.31471.9556-1.43913.514-0.3092-0.8371-0.72510.43710.02820.08950.20070.56930.19420.17770.02310.02190.18330.05230.1822-0.313530.015254.8058
91.13490.0619-0.60230.9224-0.1272.46330.0055-0.00710.01160.07140.0198-0.0348-0.00650.0555-0.02240.04390.0165-0.00790.05430.0020.07368.433939.39143.0303
103.9080.80970.48277.2298-6.46217.85930.1272-0.29020.47240.662-0.3095-0.0656-0.75810.22110.12560.28530.0208-0.01170.1712-0.02190.16484.818744.375656.6951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 282 through 300 )
2X-RAY DIFFRACTION2chain 'A' and (resid 301 through 373 )
3X-RAY DIFFRACTION3chain 'A' and (resid 374 through 390 )
4X-RAY DIFFRACTION4chain 'A' and (resid 391 through 411 )
5X-RAY DIFFRACTION5chain 'A' and (resid 412 through 427 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 20 )
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 42 )
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 86 )
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 94 )

+
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://pdbjlvh1.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