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- PDB-6ojx: PilT4 from Geobacter metallireducens bound to ATP -

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Basic information

Entry
Database: PDB / ID: 6ojx
TitlePilT4 from Geobacter metallireducens bound to ATP
ComponentsTwitching motility pilus retraction ATPase
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Twitching motility pilus retraction ATPase
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,74117
Polymers128,6503
Non-polymers2,09114
Water19,7981099
1
A: Twitching motility pilus retraction ATPase
B: Twitching motility pilus retraction ATPase
hetero molecules

A: Twitching motility pilus retraction ATPase
B: Twitching motility pilus retraction ATPase
hetero molecules

A: Twitching motility pilus retraction ATPase
B: Twitching motility pilus retraction ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,60636
Polymers257,3006
Non-polymers4,30630
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
2
C: Twitching motility pilus retraction ATPase
hetero molecules

C: Twitching motility pilus retraction ATPase
hetero molecules

C: Twitching motility pilus retraction ATPase
hetero molecules

C: Twitching motility pilus retraction ATPase
hetero molecules

C: Twitching motility pilus retraction ATPase
hetero molecules

C: Twitching motility pilus retraction ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,23430
Polymers257,3006
Non-polymers3,93424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
Unit cell
Length a, b, c (Å)190.187, 190.187, 60.455
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Twitching motility pilus retraction ATPase


Mass: 42883.379 Da / Num. of mol.: 3
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1099 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1mM ATP 1mM MgCl2 4.5 % (w/v) PEG4000 50 mM MES pH 6 100 mM MgCl2 100 mM NaCl 25 mM Hepes pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.892→48 Å / Num. obs: 99891 / % possible obs: 100 % / Redundancy: 10.4 % / Net I/σ(I): 10.6
Reflection shellResolution: 1.892→2 Å / Num. unique obs: 9942

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JVV

3jvv


Resolution: 1.892→47.547 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 1167 1.17 %
Rwork0.1843 --
obs0.1846 99843 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.892→47.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8219 0 128 1099 9446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028728
X-RAY DIFFRACTIONf_angle_d0.53511905
X-RAY DIFFRACTIONf_dihedral_angle_d13.6365368
X-RAY DIFFRACTIONf_chiral_restr0.0421389
X-RAY DIFFRACTIONf_plane_restr0.0041520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8919-1.9780.30741470.284312185X-RAY DIFFRACTION100
1.978-2.08220.27451480.239112281X-RAY DIFFRACTION100
2.0822-2.21270.23621420.209512299X-RAY DIFFRACTION100
2.2127-2.38350.23251470.177912256X-RAY DIFFRACTION100
2.3835-2.62340.21991440.188112337X-RAY DIFFRACTION100
2.6234-3.0030.24861420.187612311X-RAY DIFFRACTION100
3.003-3.78320.2161460.175612410X-RAY DIFFRACTION100
3.7832-47.56170.1751510.169912597X-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)
10.13070.126-0.0450.14040.01290.27070.00880.0606-0.4684-0.1683-0.04120.42320.3177-0.00880.00010.4420.0115-0.08540.3999-0.04640.4793159.065975.2143-24.5626
21.0638-0.27990.84050.63390.28971.1690.01070.1995-0.0281-0.1273-0.03190.12490.0378-0.1535-00.43780.0366-0.06120.4109-0.00690.3673165.227182.236-26.4834
30.10760.14990.10670.92520.45310.43410.30270.2382-0.29370.1549-0.4170.6065-0.0238-0.6395-0.00180.44850.0517-0.02350.6660.02470.5815146.975892.7435-5.2752
40.4404-0.13450.57780.9625-0.34770.92010.13520.0523-0.0806-0.0171-0.01140.14980.2012-0.104300.30760.0539-0.00460.35480.03040.3896154.253100.5036-13.3033
51.0533-0.1890.29260.6731-0.26751.2713-0.02510.01830.0750.1764-0.036-0.2974-0.09190.0171-00.33660.0415-0.04870.32440.01580.3591165.5619104.3036-3.9338
60.7462-0.0049-0.35840.1834-0.12090.51480.0691-0.3755-0.03570.706-0.13560.1860.2967-0.313-00.667-0.0198-0.04170.49530.04770.3916157.931592.39269.6204
70.9629-0.4869-1.37920.28950.88643.2883-0.2509-0.2616-0.16420.9489-0.2191-0.43460.55410.0391-0.76960.8606-0.0563-0.12980.40540.20690.6548159.203577.548710.8947
80.12820.0772-0.08490.2445-0.07270.30270.01960.11480.057-0.0290.05560.35210.0203-0.213-00.31010.0543-0.03390.42290.03470.3526144.7418119.4906-24.5674
90.8245-0.16140.50271.352-0.66691.21620.06070.13410.0099-0.1757-0.0815-0.02580.0620.013100.32370.0769-0.00030.40590.02540.2988153.7138117.5511-26.3038
101.2960.6611-0.21581.0795-0.36861.47270.0286-0.10120.0157-0.04410.0004-0.0741-0.09380.1605-0.00030.25370.04570.00660.37710.00650.3278167.3065132.6087-7.5211
111.0576-0.3806-0.22620.64990.22850.39930.0904-0.6869-0.07560.2606-0.12370.0924-0.02030.0192-0.00750.3172-0.0054-0.01960.58890.08380.2812155.3243126.46629.9778
120.29530.07570.10480.11220.09620.3229-0.0092-0.2007-0.31030.10020.04110.17180.1336-0.142100.3607-0.0005-0.01670.30940.04610.34380.6659120.51623.7844
131.0098-0.53610.28890.8365-0.44550.9979-0.0495-0.14470.03690.17310.0592-0.1320.0466-0.003800.31170.0025-0.03880.26110.00050.275683.468129.63125.8438
141.4261.4104-0.65461.8486-0.82430.5835-0.6111-0.1881-0.3246-0.20790.3266-0.20630.71950.1087-0.06030.41260.094-0.03020.36860.01590.4031101.4825118.6459-15.0583
151.4840.52780.37780.8110.16680.8088-0.09890.09650.1418-0.0930.11810.0266-0.03520.0529-00.2653-0.0065-0.02050.22630.00790.2857102.1874134.8314-16.3715
160.71180.0347-0.26430.5108-0.18220.6485-0.50450.49540.139-0.76050.42150.22040.1751-0.0616-0.10150.5143-0.1088-0.12790.4190.02980.374787.5188121.4047-31.5128
170.00210.0109-0.0040.0106-0.01220.0124-0.05440.0995-0.11030.04510.15460.35140.5307-0.38560.00010.41820.0074-0.03980.410.06130.4585157.651386.1002-10.3061
180.0566-0.0105-0.01560.02020.01850.01590.00110.23690.1256-0.1357-0.08760.2376-0.1025-0.29350.00020.31650.05680.03570.39060.03560.3711153.521126.0623-10.3144
190.0065-0.001-0.00010.03160.02510.03480.07870.0158-0.0460.2169-0.1355-0.00440.2751-0.29180.00020.34590.0002-0.04750.28510.01520.346590.7373124.8204-10.4061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:27 )A1 - 27
2X-RAY DIFFRACTION2( CHAIN A AND RESID 28:100 )A28 - 100
3X-RAY DIFFRACTION3( CHAIN A AND RESID 101:121 )A101 - 121
4X-RAY DIFFRACTION4( CHAIN A AND RESID 122:185 )A122 - 185
5X-RAY DIFFRACTION5( CHAIN A AND RESID 186:271 )A186 - 271
6X-RAY DIFFRACTION6( CHAIN A AND RESID 272:328 )A272 - 328
7X-RAY DIFFRACTION7( CHAIN A AND RESID 329:353 )A329 - 353
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1:27 )B1 - 27
9X-RAY DIFFRACTION9( CHAIN B AND RESID 28:100 )B28 - 100
10X-RAY DIFFRACTION10( CHAIN B AND RESID 101:271 )B101 - 271
11X-RAY DIFFRACTION11( CHAIN B AND RESID 272:354 )B272 - 354
12X-RAY DIFFRACTION12( CHAIN C AND RESID 1:27 )C1 - 27
13X-RAY DIFFRACTION13( CHAIN C AND RESID 28:100 )C28 - 100
14X-RAY DIFFRACTION14( CHAIN C AND RESID 101:121 )C101 - 121
15X-RAY DIFFRACTION15( CHAIN C AND RESID 122:309 )C122 - 309
16X-RAY DIFFRACTION16( CHAIN C AND RESID 310:354 )C310 - 354
17X-RAY DIFFRACTION17( CHAIN A AND RESID 406:406 )A406
18X-RAY DIFFRACTION18( CHAIN B AND RESID 404:404 )B404
19X-RAY DIFFRACTION19( CHAIN C AND RESID 404:404 )C404

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