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- PDB-6okv: PilT4 from Geobacter metallireducens bound to AMP-PNP: C2ccocco c... -

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Basic information

Entry
Database: PDB / ID: 6okv
TitlePilT4 from Geobacter metallireducens bound to AMP-PNP: C2ccocco conformation
ComponentsTwitching motility pilus retraction ATPase
KeywordsMOTOR PROTEIN / T4P / type IV pilus / motor / ATPase
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
Pilus retraction protein PilT/PilU / : / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Twitching motility pilus retraction ATPase
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.007 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 15, 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 / 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_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
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)260,27716
Polymers257,3006
Non-polymers2,97610
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, CryoEM evidence for hexamer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22580 Å2
ΔGint-52 kcal/mol
Surface area82600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.510, 127.130, 187.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Twitching motility pilus retraction ATPase


Mass: 42883.379 Da / Num. of mol.: 6
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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39VU6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 1 mM AMP-PNP (ANP) 1 mM MgCl2 100 mM NaCl 25 mM Hepes pH 8.0 1 % (w/v) benzamidine-HCl 50 mM Hepes pH 7.9 100 mM Ammonium acetate 8.75 % (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: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4→49.255 Å / Num. obs: 12264 / % possible obs: 98 % / Redundancy: 3.3 % / CC1/2: 0.989 / Net I/σ(I): 4
Reflection shellResolution: 4→4.1 Å / Num. unique obs: 1745 / CC1/2: 0.579

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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: 4.007→49.255 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.57
RfactorNum. reflection% reflection
Rfree0.2798 590 4.82 %
Rwork0.2435 --
obs0.2451 12240 60.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.007→49.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16007 0 182 0 16189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916476
X-RAY DIFFRACTIONf_angle_d1.05922461
X-RAY DIFFRACTIONf_dihedral_angle_d14.3426078
X-RAY DIFFRACTIONf_chiral_restr0.0542692
X-RAY DIFFRACTIONf_plane_restr0.0062904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0068-4.40980.3298440.30421040X-RAY DIFFRACTION22
4.4098-5.04730.29311230.25352161X-RAY DIFFRACTION46
5.0473-6.3570.36891820.29213476X-RAY DIFFRACTION72
6.357-49.25870.2252410.21124973X-RAY DIFFRACTION99
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)
10.0422-0.3925-0.09864.08540.97630.24170.1083-0.0641-0.2929-0.4320.5034-1.29550.46720.2689-0.48491.2486-0.4917-0.3512.84270.70540.8791-0.5579-105.43231.1522
21.1301-0.7039-0.62620.89960.43310.3585-0.50320.5117-0.66310.5006-0.27380.46760.2983-0.32130.54730.9335-0.50750.08871.65760.78421.414-11.2503-105.08072.7411
30.95221.5346-0.60562.5252-0.97060.38650.6911-0.3530.24811.35630.07140.0527-1.31290.3672-0.78250.712-0.06080.11421.0105-0.51340.8537-47.1835-71.1649-32.5402
47.4565-0.85483.01444.24381.60689.2624-1.11140.60570.90920.5699-1.1891.27320.3085-1.24661.25590.3022-0.6110.17940.9957-0.4570.6514-50.0689-76.2122-36.21
55.00130.45650.56642.5853-0.192.00490.5138-1.2361-0.5010.3064-0.0852-0.14530.7881-0.5629-0.26220.8306-0.3666-0.23460.41020.29080.5795-28.8425-88.2323-23.3595
61.1099-1.20010.42161.82920.06992.0743-0.4321-0.06740.06030.68830.30730.0457-1.0927-0.79210.16640.235-0.121-0.00711.0291-0.24410.4837-34.7807-72.5973-73.4825
70.10510.12410.030.20880.06960.12790.0090.08180.11720.13080.17640.5839-0.12240.03520.14492.34280.6188-0.0457-0.87310.8260.4789-45.4824-94.3085-56.0786
83.55130.1027-0.59863.6235-0.79741.7978-0.0044-0.1846-1.1437-0.9271-0.6791-0.67660.55790.24480.45811.2199-0.02740.20880.50450.2590.8729-31.88-95.1149-52.3419
94.682-2.1472-0.5012.13910.70672.99261.18461.01961.311-0.895-0.2883-0.8183-0.83660.964-0.16391.21020.64810.36661.2560.58651.09656.0444-70.8598-92.5967
104.538-1.7153-0.35321.88610.62392.63380.42170.5478-0.2484-0.3593-0.65310.11990.14020.43920.24480.70150.0795-0.08040.514-0.14280.617-12.4242-87.1523-80.5892
110.02750.00390.10150.04910.13710.660.0120.07310.01760.76860.37451.13480.19330.1474-0.21.1630.7283-0.17290.1558-1.06021.634-8.4801-105.9451-94.9792
120.06320.07990.18420.6113-0.17030.620.5422-0.7034-0.5310.29630.4637-1.00991.1650.4824-0.95081.26780.2517-0.48162.136-0.29731.18762.3558-105.5253-96.8233
132.4822-0.13751.23862.8177-0.8932.1531-0.4629-1.02630.6214-0.254-0.5116-0.5801-0.1222-0.59770.83420.5699-0.17910.07431.46320.31190.678738.5455-71.1633-61.6006
140.8379-0.3783-0.32330.62450.17760.14570.28450.15941.3350.07-0.5852-0.7948-0.13050.26850.03831.2935-0.10740.56742.07581.12441.079241.5666-76.8546-57.7253
150.31780.1001-0.09350.0678-0.0920.2620.91220.40670.247-0.19960.3473-0.05040.197-0.4669-0.56931.0704-0.69330.28721.50891.57771.574626.5474-61.4465-54.8862
163.4242-0.2010.92091.14090.17852.54190.29080.1347-0.37-0.11450.0410.16330.4995-0.908-0.2040.6202-0.22020.03321.08250.29570.521319.1419-90.884-71.4247
170.3373-0.0777-0.13522.2316-0.94970.9343-0.19440.1592-0.02860.7161-0.2974-1.2584-0.15661.82970.24090.8030.0654-0.22041.6672-0.03880.873530.9476-74.4372-13.3638
180.55430.59260.24040.57360.24130.1048-0.4490.28690.6099-0.51690.11570.4795-0.7858-0.03070.19841.2959-0.6344-0.08790.04471.0031.112720.6952-65.2229-25.9071
190.2565-0.08850.42150.5065-0.14710.7059-0.12290.53090.567-0.165-0.2447-0.0506-0.64030.12170.03221.0275-0.67640.02091.07210.27620.884725.4299-74.0946-24.8144
200.5075-0.1620.10890.1032-0.22040.6824-0.3696-0.66130.0184-0.1284-0.09560.3162-0.5954-0.3360.38160.6241.38340.16530.56220.20560.904837.3606-93.9407-37.2777
210.40520.39050.48110.59650.40120.5632-1.11090.60850.51860.2003-0.4951-1.9518-0.169-0.22520.79230.7274-0.8106-0.4903-0.2576-0.57020.57930.2997-91.2666-41.1438
220.97390.65870.09891.5952-0.26181.29690.49440.22081.1265-0.71010.22850.61350.49970.55810.08640.4741-0.16910.0331.60460.47220.76724.5643-82.7146-46.0949
231.12510.5126-0.03011.96150.55291.1308-0.27971.03171.43080.1815-0.15871.4139-0.12090.12410.37460.7363-0.26280.22111.5656-0.24661.275814.5939-97.7457-43.2987
241.84660.97960.86430.64650.43730.8491-0.34-0.2329-1.4522-0.9111-0.0117-0.4045-0.5298-0.2622-0.1491.0242-0.1795-0.14221.396-0.31261.088424.7994-108.0896-33.0624
250.84150.634-0.02711.92271.11171.41241.0003-0.20270.25281.2169-0.16760.11770.2107-0.2967-0.33320.4558-0.06010.13310.8564-0.17940.5655-14.9439-68.4355-0.7321
260.07420.23170.2090.6990.73670.86840.157-0.1310.0204-0.10640.3339-1.6127-0.2182-0.003-0.24031.45150.68990.15380.79370.42731.3837-8.5658-62.0646-16.8284
270.76260.313-1.13270.8823-0.51221.82360.253-0.07920.07720.0918-0.1482-0.40080.06050.1520.06080.2945-0.5951-0.25690.4871-1.48141.2378-7.3485-70.5509-11.0374
281.28080.8506-0.57990.5658-0.33632.37670.3326-0.62380.46750.3726-0.8620.5891-0.06051.10130.70320.50740.0620.05520.99350.34350.61288.6267-90.13470.9571
290.19330.06240.14080.05260.01410.1368-0.61540.3151-0.1447-0.017-0.0283-0.2729-0.4510.30740.2517-0.02431.1222-0.4112-0.45471.38450.51178.689-89.7874-7.3695
300.04460.03060.03580.5157-0.5481.409-0.913-1.027-0.42650.9257-0.20550.91410.12081.34640.64060.60610.93740.01280.97760.24450.789312.2109-78.6286-12.5536
310.76660.05780.84933.5749-0.92141.2112-0.2556-0.1435-0.2408-0.6240.59130.425-0.0378-0.0303-0.190.43980.18090.2461.0092-0.18910.668111.9494-83.8515-22.0655
321.3507-0.27150.45390.60460.40820.83330.09120.4169-0.8637-0.14581.03920.6820.4142-0.3101-0.52750.7165-0.13960.27230.32430.6480.60127.9098-92.6569-19.6908
331.2808-0.35271.68742.1963-0.45963.37010.1862-0.2592-0.6762-1.33220.6979-0.20670.6285-0.7142-0.50360.6856-0.2135-0.02470.4309-0.02581.3362.6375-100.1128-19.4238
341.49560.73831.52370.92560.97731.55770.2147-0.5451-1.46770.18421.2848-0.46110.38780.3517-1.12481.55160.10570.01280.4432-0.02161.34111.947-105.4951-9.1991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 310 through 328 )
2X-RAY DIFFRACTION2chain 'D' and (resid 329 through 353 )
3X-RAY DIFFRACTION3chain 'E' and (resid 1 through 27 )
4X-RAY DIFFRACTION4chain 'E' and (resid 28 through 44 )
5X-RAY DIFFRACTION5chain 'E' and (resid 45 through 353 )
6X-RAY DIFFRACTION6chain 'F' and (resid 2 through 100 )
7X-RAY DIFFRACTION7chain 'F' and (resid 101 through 121 )
8X-RAY DIFFRACTION8chain 'F' and (resid 122 through 353 )
9X-RAY DIFFRACTION9chain 'A' and (resid 2 through 44 )
10X-RAY DIFFRACTION10chain 'A' and (resid 45 through 309 )
11X-RAY DIFFRACTION11chain 'A' and (resid 310 through 328 )
12X-RAY DIFFRACTION12chain 'A' and (resid 329 through 353 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 27 )
14X-RAY DIFFRACTION14chain 'B' and (resid 28 through 44 )
15X-RAY DIFFRACTION15chain 'B' and (resid 45 through 67 )
16X-RAY DIFFRACTION16chain 'B' and (resid 68 through 351 )
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 44 )
18X-RAY DIFFRACTION18chain 'C' and (resid 45 through 67 )
19X-RAY DIFFRACTION19chain 'C' and (resid 68 through 100 )
20X-RAY DIFFRACTION20chain 'C' and (resid 101 through 121 )
21X-RAY DIFFRACTION21chain 'C' and (resid 122 through 151 )
22X-RAY DIFFRACTION22chain 'C' and (resid 152 through 233 )
23X-RAY DIFFRACTION23chain 'C' and (resid 234 through 271 )
24X-RAY DIFFRACTION24chain 'C' and (resid 272 through 352 )
25X-RAY DIFFRACTION25chain 'D' and (resid -4 through 44 )
26X-RAY DIFFRACTION26chain 'D' and (resid 45 through 67 )
27X-RAY DIFFRACTION27chain 'D' and (resid 68 through 100 )
28X-RAY DIFFRACTION28chain 'D' and (resid 101 through 121 )
29X-RAY DIFFRACTION29chain 'D' and (resid 122 through 151 )
30X-RAY DIFFRACTION30chain 'D' and (resid 152 through 185 )
31X-RAY DIFFRACTION31chain 'D' and (resid 186 through 208 )
32X-RAY DIFFRACTION32chain 'D' and (resid 209 through 233 )
33X-RAY DIFFRACTION33chain 'D' and (resid 234 through 271 )
34X-RAY DIFFRACTION34chain 'D' and (resid 272 through 309 )

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