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- PDB-4zv0: Structure of Tse6 in complex with Tsi6 -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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 )

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