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- PDB-6ojy: Methylated PilT4 from Geobacter metallireducens bound to sulfate:... -

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Basic information

Entry
Database: PDB / ID: 6ojy
TitleMethylated PilT4 from Geobacter metallireducens bound to sulfate: C3ocococ conformation
Components(Twitching motility pilus retraction ...) x 5
KeywordsMOTOR PROTEIN / T4P / ATPase / type IV pilus / motor
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
Pilus retraction protein PilT/PilU / Beta-Lactamase - #90 / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich ...Pilus retraction protein PilT/PilU / Beta-Lactamase - #90 / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Twitching motility pilus retraction ATPase
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMcCallum, M. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2019
Title: Multiple conformations facilitate PilT function in the type IV pilus.
Authors: Matthew McCallum / Samir Benlekbir / Sheryl Nguyen / Stephanie Tammam / John L Rubinstein / Lori L Burrows / P Lynne Howell /
Abstract: Type IV pilus-like systems are protein complexes that polymerize pilin fibres. They are critical for virulence in many bacterial pathogens. Pilin polymerization and depolymerization are powered by ...Type IV pilus-like systems are protein complexes that polymerize pilin fibres. They are critical for virulence in many bacterial pathogens. Pilin polymerization and depolymerization are powered by motor ATPases of the PilT/VirB11-like family. This family is thought to operate with C symmetry; however, most of these ATPases crystallize with either C or C symmetric conformations. The relevance of these conformations is unclear. Here, we determine the X-ray structures of PilT in four unique conformations and use these structures to classify the conformation of available PilT/VirB11-like family member structures. Single particle electron cryomicroscopy (cryoEM) structures of PilT reveal condition-dependent preferences for C C, and C conformations. The physiologic importance of these conformations is validated by coevolution analysis and functional studies of point mutants, identifying a rare gain-of-function mutation that favours the C conformation. With these data, we propose a comprehensive model of PilT function with broad implications for PilT/VirB11-like family members.
History
DepositionApr 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Twitching motility pilus retraction ATPase
B: Twitching motility pilus retraction ATPase
C: Twitching motility pilus retraction ATPase
D: Twitching motility pilus retraction ATPase
E: Twitching motility pilus retraction ATPase
F: Twitching motility pilus retraction ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,17412
Polymers257,5986
Non-polymers5766
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, cryoEM evidence of hexamer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17820 Å2
ΔGint-128 kcal/mol
Surface area84740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.800, 119.010, 178.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Twitching motility pilus retraction ... , 5 types, 6 molecules ABCDEF

#1: Protein Twitching motility pilus retraction ATPase


Mass: 42937.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: pilT-4, Gmet_1394 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q39VU6
#2: Protein Twitching motility pilus retraction ATPase


Mass: 42937.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: pilT-4, Gmet_1394 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q39VU6
#3: Protein Twitching motility pilus retraction ATPase


Mass: 42937.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: pilT-4, Gmet_1394 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q39VU6
#4: Protein Twitching motility pilus retraction ATPase


Mass: 42937.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: pilT-4, Gmet_1394 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q39VU6
#5: Protein Twitching motility pilus retraction ATPase


Mass: 42910.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: pilT-4, Gmet_1394 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q39VU6

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Non-polymers , 2 types, 197 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25 mM Hepes pH 7 75 mM NaCl 5 % (v/v) glycerol 100 mM ammonium sulphate 50 mM Bis-Tris-HCl pH 6.5 12.5% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.3→48.558 Å / Num. obs: 37753 / % possible obs: 100 % / Redundancy: 7.4 % / Rpim(I) all: 0.067 / Net I/σ(I): 12.6
Reflection shellResolution: 3.3→3.4 Å / Num. unique obs: 3658 / Rpim(I) all: 0.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JVV

3jvv


Resolution: 3.3→48.558 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.34
RfactorNum. reflection% reflection
Rfree0.246 1899 5.04 %
Rwork0.2088 --
obs0.2107 37693 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→48.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16197 0 30 191 16418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516551
X-RAY DIFFRACTIONf_angle_d0.89422499
X-RAY DIFFRACTIONf_dihedral_angle_d13.13410120
X-RAY DIFFRACTIONf_chiral_restr0.0532669
X-RAY DIFFRACTIONf_plane_restr0.0062925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.38250.31691320.29092482X-RAY DIFFRACTION98
3.3825-3.4740.30171310.28012511X-RAY DIFFRACTION100
3.474-3.57620.29621520.26872503X-RAY DIFFRACTION100
3.5762-3.69160.33411440.25062525X-RAY DIFFRACTION100
3.6916-3.82340.25141220.24392521X-RAY DIFFRACTION100
3.8234-3.97650.28131190.22472572X-RAY DIFFRACTION100
3.9765-4.15730.24481500.21062514X-RAY DIFFRACTION100
4.1573-4.37640.23551130.19792569X-RAY DIFFRACTION100
4.3764-4.65040.23821360.17712552X-RAY DIFFRACTION100
4.6504-5.00910.18921340.16692559X-RAY DIFFRACTION100
5.0091-5.51260.25041360.20212581X-RAY DIFFRACTION100
5.5126-6.30880.26971290.22182580X-RAY DIFFRACTION100
6.3088-7.94280.25351490.21082606X-RAY DIFFRACTION100
7.9428-48.56290.1841520.15882719X-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)
14.0765-1.93531.65324.2698-1.3034.35850.1678-0.4253-0.63090.08820.01730.53810.2916-0.5612-0.21170.4721-0.06470.18110.4350.10330.6518-33.7409-13.855155.555
21.0982-0.4955-1.24295.52162.80135.6330.018-0.07450.2025-0.11580.17620.7278-0.1127-0.6082-0.15060.28530.00490.04770.37270.08490.5299-39.5301-3.663737.0479
32.0939-0.2842-0.65224.38461.57855.13750.08380.00010.0573-0.20320.1464-0.0029-0.90130.2916-0.21890.48550.05920.09660.3322-0.02660.4442-31.79929.346635.5583
40.46730.4875-0.92082.02891.06994.5274-0.2840.1757-0.01320.7686-0.0480.3779-1.3084-1.23430.34231.5560.45840.23710.8169-0.10711.004-40.277523.176841.6375
50.4861-1.67370.27575.7288-0.85231.1450.0965-0.03940.51771.75340.13580.0821-1.6396-1.0005-0.22391.79170.40240.430.8050.08020.8042-39.612821.084157.9663
67.55920.1907-0.37729.49620.78697.2465-0.27870.9308-1.2877-1.4668-0.14581.86380.4705-0.66980.40660.7128-0.0971-0.20970.5209-0.11290.8476-44.4647-20.069418.4478
77.6827-0.5027-0.94126.53010.64865.8077-0.51120.5623-0.2614-0.87190.06690.12640.3168-0.24030.44410.4961-0.152-0.06660.3273-0.01520.4614-35.7571-18.367821.5385
85.3952.1503-4.62454.3766-2.09944.585-0.01011.3030.6312-0.72220.21580.6454-0.157-0.694-0.17540.66670.0817-0.0921.12850.25350.5791-31.03391.2289-1.1353
94.9427-0.331-3.69382.0410.04195.24430.85070.06680.4723-0.0915-0.26560.1182-1.3744-0.9445-0.54540.52840.06260.13670.62490.11960.5609-24.37850.04123.134
106.09330.5086-0.62876.8093-1.5854.98520.193-0.11980.1913-0.12320.2374-0.1736-0.1283-0.1482-0.36590.4692-0.11570.02460.4475-0.03920.2511-16.0156-7.04656.548
116.4812-3.1965-1.53322.4534-1.47816.1637-0.1958-1.04471.16370.68050.3957-0.0113-1.80880.9072-0.19421.0796-0.1910.3520.7223-0.32111.0947-14.44149.619813.9648
128.3441.12262.31527.05292.91956.64270.9057-0.95391.6085-0.5265-0.12-0.5451-2.0336-0.8198-0.80841.48110.09860.55570.9129-0.00971.1064-23.755316.04828.4765
137.79495.41660.32654.88961.81742.2543-0.8323-1.4951.7585-0.15430.3921.1081-0.8477-1.1070.43511.48930.80570.19651.59040.11631.1679-36.390818.169610.2042
143.12342.6082-1.04973.3593-0.7671.6598-0.64170.5541-1.0041-0.9290.0822-0.90770.89550.09010.56140.8632-0.0010.20310.6262-0.13110.6263-2.9927-16.5144-5.9082
154.1914-1.2262.28165.6151-1.44815.1091-0.171-0.07340.69240.40370.08790.1616-0.2277-0.61440.11090.2867-0.03480.13450.5811-0.00370.415310.91313.68751.084
162.00024.8566.85134.45736.58859.7623-0.75372.34590.9881-1.22660.3946-0.3961-2.79690.34120.36761.04690.2171-0.10361.13730.42891.04174.680315.4923-15.999
178.9470.48212.0267.23090.71695.1835-0.61821.22331.7571-0.51310.07961.0949-1.2717-1.01570.5390.73860.013-0.11051.04840.33841.1016-6.374515.3251-17.2186
187.42620.3809-0.25264.80170.27294.13320.32830.2862-0.33170.0411-0.158-0.39220.82890.0268-0.1590.68760.059-0.01390.3812-0.13250.338628.9266-17.20528.406
194.42660.13821.01218.0716-0.78853.414-0.14150.18010.1655-0.5060.13660.09780.02270.02920.05170.6151-0.1128-0.0710.3088-0.05590.268229.75672.276629.3648
207.0363-0.07270.48414.9119-0.23593.2461-0.96010.71771.8274-0.95880.24390.3062-0.40530.13270.72630.9788-0.174-0.22220.50710.09850.948428.766821.671924.7295
212.6995-2.04570.33292.21110.71541.4694-0.50550.79570.9169-1.00740.80460.035-0.6074-0.2136-0.29171.9476-0.6059-0.40431.17860.50771.184230.498321.62188.3525
223.346-0.2301-0.42044.18831.49851.78040.0829-0.8084-1.07560.8542-0.0975-0.53640.78290.2824-0.00181.01780.0853-0.25630.52350.20670.768936.1261-17.673946.4071
236.07173.0556-1.6574.0574-0.94842.0180.0559-0.014-0.1918-0.06350.07250.09050.10530.1674-0.12260.33420.0389-0.07630.3841-0.0490.249321.21164.797160.2013
248.9175-0.3306-2.20385.92861.79934.44350.58870.15251.2349-0.0883-0.0315-0.3539-0.40740.1755-0.55870.46070.03550.08950.35070.04440.434234.409222.865857.3062
254.60471.17170.10473.21631.09396.58020.493-0.7298-1.02520.4624-0.20460.41890.6806-0.268-0.3010.5669-0.0491-0.12660.50190.23470.82925.6969-14.542271.5631
265.30510.66870.81984.8741-0.15653.7896-0.1015-0.47840.47060.36890.1983-0.2582-0.09710.0246-0.0940.370.06940.03850.344-0.04960.5394-15.5363-0.416961.6015
275.13971.97261.66193.78910.97187.2152-0.02930.22311.11740.1886-0.10070.0374-0.95060.09010.11070.5140.0081-0.00080.47190.03121.0471-9.212617.162859.0858
281.73550.51951.51812.04514.26212.00210.32560.50870.2283-0.06511.0362-0.309-0.51882.1418-1.36680.9083-0.21670.14511.1364-0.25051.12593.043222.934172.0178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 121 )
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 185 )
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 300 )
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 318 )
5X-RAY DIFFRACTION5chain 'A' and (resid 319 through 354 )
6X-RAY DIFFRACTION6chain 'B' and (resid -4 through 27 )
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 100 )
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 121 )
9X-RAY DIFFRACTION9chain 'B' and (resid 122 through 151 )
10X-RAY DIFFRACTION10chain 'B' and (resid 152 through 233 )
11X-RAY DIFFRACTION11chain 'B' and (resid 234 through 270 )
12X-RAY DIFFRACTION12chain 'B' and (resid 271 through 309 )
13X-RAY DIFFRACTION13chain 'B' and (resid 310 through 350 )
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 130 )
15X-RAY DIFFRACTION15chain 'C' and (resid 131 through 308 )
16X-RAY DIFFRACTION16chain 'C' and (resid 309 through 328 )
17X-RAY DIFFRACTION17chain 'C' and (resid 329 through 353 )
18X-RAY DIFFRACTION18chain 'D' and (resid 3 through 100 )
19X-RAY DIFFRACTION19chain 'D' and (resid 101 through 288 )
20X-RAY DIFFRACTION20chain 'D' and (resid 289 through 328 )
21X-RAY DIFFRACTION21chain 'D' and (resid 329 through 354 )
22X-RAY DIFFRACTION22chain 'E' and (resid 2 through 100 )
23X-RAY DIFFRACTION23chain 'E' and (resid 101 through 288 )
24X-RAY DIFFRACTION24chain 'E' and (resid 289 through 357 )
25X-RAY DIFFRACTION25chain 'F' and (resid 1 through 100 )
26X-RAY DIFFRACTION26chain 'F' and (resid 101 through 233 )
27X-RAY DIFFRACTION27chain 'F' and (resid 234 through 328 )
28X-RAY DIFFRACTION28chain 'F' and (resid 329 through 352 )

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