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- PDB-4zv4: Structure of Tse6 in complex with EF-Tu -

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Basic information

Entry
Database: PDB / ID: 4zv4
TitleStructure of Tse6 in complex with EF-Tu
Components
  • Elongation factor Tu
  • Tse6
KeywordsTRANSLATION / T6SS effector / translation elongation factor
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 / translational elongation / translation elongation factor activity / GTPase activity / GTP binding ...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 / translational elongation / translation elongation factor activity / GTPase activity / GTP binding / membrane / cytoplasm
Similarity search - Function
Bacterial toxin 46 / Bacterial toxin 46 / PAAR motif / PAAR motif / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal ...Bacterial toxin 46 / Bacterial toxin 46 / PAAR motif / PAAR motif / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu / NAD(P)(+) glycohydrolase toxin Tse6
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.504 Å
AuthorsWhitney, J.C. / Sawai, S. / Robinson, H. / 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 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu
C: Tse6
D: Tse6
B: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1738
Polymers129,2384
Non-polymers9354
Water00
1
A: Elongation factor Tu
C: Tse6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0864
Polymers64,6192
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Tse6
B: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0864
Polymers64,6192
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.109, 176.109, 86.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Elongation factor Tu / EF-Tu


Mass: 44494.699 Da / Num. of mol.: 2
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: tufA, PA4265, tufB, PA4277 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: P09591
#2: Protein Tse6


Mass: 20124.150 Da / Num. of mol.: 2 / Fragment: unp residues 265-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (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
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 22% (w/v) PEG 3350, 0.2M ammonium formate pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 32569 / % possible obs: 100 % / Redundancy: 27.6 % / Net I/σ(I): 39.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFC

1efc


Resolution: 3.504→48.844 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2834 1637 5.03 %
Rwork0.2299 --
obs0.2326 32568 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.504→48.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8003 0 58 0 8061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038228
X-RAY DIFFRACTIONf_angle_d0.70711242
X-RAY DIFFRACTIONf_dihedral_angle_d13.1532863
X-RAY DIFFRACTIONf_chiral_restr0.0281289
X-RAY DIFFRACTIONf_plane_restr0.0041489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5037-3.60680.38931350.32412580X-RAY DIFFRACTION99
3.6068-3.72320.3511290.28332558X-RAY DIFFRACTION100
3.7232-3.85620.3211420.25892588X-RAY DIFFRACTION100
3.8562-4.01050.33441370.25872563X-RAY DIFFRACTION100
4.0105-4.1930.35111370.24022588X-RAY DIFFRACTION100
4.193-4.41390.2711400.21672567X-RAY DIFFRACTION100
4.4139-4.69020.27291360.19892576X-RAY DIFFRACTION100
4.6902-5.0520.23241380.19962604X-RAY DIFFRACTION100
5.052-5.55980.22811310.21742554X-RAY DIFFRACTION100
5.5598-6.36280.30061430.24942583X-RAY DIFFRACTION100
6.3628-8.01070.31511320.24262590X-RAY DIFFRACTION100
8.0107-48.84860.24561370.20592580X-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)
11.38960.285-1.8011.8128-0.56911.37920.11810.0264-0.27330.5203-0.1704-0.1258-0.34450.14620.00390.5261-0.0242-0.10150.30070.07420.3997-24.703214.1473-6.5981
22.4587-0.8760.42671.48520.11911.128-0.1333-0.1004-0.2905-0.1846-0.010.3835-0.0849-0.419900.5507-0.00180.02940.5392-0.12070.6453-55.033323.5131-9.0516
30.48850.3098-0.75631.2726-1.31011.452-0.11960.22810.17060.0320.2148-0.0840.5221-0.458900.7551-0.05740.00420.78070.02120.503-64.5404-34.690418.6753
40.0549-0.0115-0.3758-0.05480.1015-0.17470.7484-0.2344-0.4627-0.1389-0.0641-0.3459-0.1994-0.023802.3920.66790.03791.2914-0.2796-0.1263-78.1004-10.966142.9298
50.0839-0.0190.0465-0.09250.07630.00740.51830.2358-0.60160.13590.46210.8177-0.2109-0.35320.04431.40991.76720.773.7869-2.11640.3868-87.169-11.224646.6983
60.57330.29050.0652-0.13580.11040.4263-0.849-0.24890.66960.16010.4515-0.3947-2.26530.1407-0.52432.72280.1195-0.2620.52490.19880.812-66.2036-5.386327.5528
70.7791-0.1627-0.33470.2041-0.04230.2419-0.2207-1.21060.096-0.0432-0.17090.46450.90890.30660.0110.87340.0938-0.00030.52940.08870.9832-22.2612-10.0496-13.0565
80.01620.0163-0.0226-0.09660.08120.0258-0.68850.1847-0.2050.3211-0.171-0.8969-0.2072-0.0995-0.00030.95-0.0535-0.03270.67170.06290.8262-27.3296-3.92155.4037
90.2635-0.0866-0.00310.2617-0.01610.4418-0.32360.1233-0.14280.24150.20230.1662-0.43040.46580.0130.86090.046-0.08710.60680.05920.9207-29.5782-8.921617.9129
10-0.02310.0315-0.00450.03170.01470.0844-0.1656-0.55060.5981-0.5256-0.1978-0.1698-0.92620.2317-0.0031.0537-0.229-0.05951.04090.3770.5565-27.1146-14.551228.2838
111.0743-0.4569-0.14940.30390.28690.37590.26930.2108-0.92521.1044-0.7356-0.22880.6262-0.421-0.07960.5742-0.05240.13130.59260.36241.0618-29.3311-23.343724.2331
120.64690.1341-0.01360.0696-0.0387-0.0309-0.11690.7266-1.26981.0687-0.54930.4739-1.44030.3132-0.01511.47420.1017-0.01550.53670.15680.4945-33.3934-12.265927.2872
130.2009-0.0140.29750.05110.1578-0.00720.2528-0.4393-0.2999-0.38410.01-0.9896-0.2010.15310.07030.7832-0.0058-0.17180.69090.21660.8163-25.9475-17.44319.2742
14-0.1635-0.0790.04930.00130.07980.0346-0.09-0.5507-0.0293-0.31280.4824-0.01510.44510.00350.00030.67260.0004-0.10221.08880.33830.7141-47.6899-31.38553.243
150.0510.9484-0.33740.3278-0.03390.8503-0.1237-0.5714-0.3124-0.66460.49020.4944-0.2052-0.19150.04860.47080.0477-0.23540.53230.17950.6805-45.7059-17.123-14.8063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 202 )
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 401 )
3X-RAY DIFFRACTION3chain 'B' and (resid 10 through 202 )
4X-RAY DIFFRACTION4chain 'B' and (resid 203 through 254 )
5X-RAY DIFFRACTION5chain 'B' and (resid 255 through 276 )
6X-RAY DIFFRACTION6chain 'B' and (resid 277 through 397 )
7X-RAY DIFFRACTION7chain 'C' and (resid 262 through 279 )
8X-RAY DIFFRACTION8chain 'C' and (resid 280 through 299 )
9X-RAY DIFFRACTION9chain 'C' and (resid 300 through 335 )
10X-RAY DIFFRACTION10chain 'C' and (resid 336 through 345 )
11X-RAY DIFFRACTION11chain 'C' and (resid 346 through 369 )
12X-RAY DIFFRACTION12chain 'C' and (resid 370 through 388 )
13X-RAY DIFFRACTION13chain 'C' and (resid 389 through 423 )
14X-RAY DIFFRACTION14chain 'D' and (resid 265 through 313 )
15X-RAY DIFFRACTION15chain 'D' and (resid 314 through 427 )

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