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- PDB-5oiu: Crystal structure of PilF type IV pilus assembly ATPase from Ther... -

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Basic information

Entry
Database: PDB / ID: 5oiu
TitleCrystal structure of PilF type IV pilus assembly ATPase from Thermus thermophilus
ComponentsType IV pilus assembly protein PilF
KeywordsMOTOR PROTEIN / ATPase / AAA+ / type IV pilus / DNA binding protein / ATP
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Beta-Lactamase - #90 / Type II secretion system protein GspE, N-terminal / MshEN domain / Type II secretion system protein GspE, N-terminal superfamily / 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 ...Beta-Lactamase - #90 / Type II secretion system protein GspE, N-terminal / MshEN domain / Type II secretion system protein GspE, N-terminal superfamily / 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 / Type IV pilus assembly ATPase PilB
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsKaruppiah, V. / Derrick, J.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust093388/Z/10/Z United Kingdom
CitationJournal: Sci Rep / Year: 2018
Title: Structural cycle of the Thermus thermophilus PilF ATPase: the powering of type IVa pilus assembly.
Authors: Richard Collins / Vijaykumar Karuppiah / C Alistair Siebert / Rana Dajani / Angela Thistlethwaite / Jeremy P Derrick /
Abstract: Type IV pili are responsible for a diverse range of functions, including twitching motility and cell adhesion. Assembly of the pilus fiber is driven by a cytoplasmic ATPase: it interacts with an ...Type IV pili are responsible for a diverse range of functions, including twitching motility and cell adhesion. Assembly of the pilus fiber is driven by a cytoplasmic ATPase: it interacts with an inner membrane complex of biogenesis proteins which, in turn, bind to nascent pilin subunits and mediate fiber assembly. Here we report the structural characterization of the PilF TFP assembly ATPase from Thermus thermophilus. The crystal structure of a recombinant C-terminal fragment of PilF revealed bound, unhydrolysed ATP, although the full length complex was enzymatically active. 3D reconstructions were carried out by single particle cryoelectron microscopy for full length apoprotein PilF and in complex with AMPPNP. The structure forms an hourglass-like shape, with the ATPase domains in one half and the N1 domains in the second half which, we propose, interact with the other pilus biogenesis components. Molecular models for both forms were generated: binding of AMPPNP causes an upward shift of the N1 domains towards the ATPase domains of ~8 Å. We advocate a model in which ATP hydrolysis is linked to displacement of the N1 domains which is associated with lifting pilin subunits out of the inner membrane, and provide the activation energy needed to form the pilus fiber.
History
DepositionJul 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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: Type IV pilus assembly protein PilF
B: Type IV pilus assembly protein PilF
C: Type IV pilus assembly protein PilF
D: Type IV pilus assembly protein PilF
E: Type IV pilus assembly protein PilF
F: Type IV pilus assembly protein PilF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,76736
Polymers258,7606
Non-polymers4,00730
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25920 Å2
ΔGint-254 kcal/mol
Surface area93520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.390, 107.660, 137.830
Angle α, β, γ (deg.)90.00, 112.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Type IV pilus assembly protein PilF


Mass: 43126.621 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0364 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLC9

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Non-polymers , 5 types, 409 molecules

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium bromide, 0.1 M Bis-Tris propane pH 6.5, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.44→95.106 Å / Num. obs: 109033 / % possible obs: 98.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.5
Reflection shellResolution: 2.44→2.5 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSZ

2gsz


Resolution: 2.44→95.106 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 5334 4.99 %
Rwork0.1904 --
obs0.1931 106789 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→95.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17940 0 210 379 18529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918408
X-RAY DIFFRACTIONf_angle_d1.05124896
X-RAY DIFFRACTIONf_dihedral_angle_d7.94212846
X-RAY DIFFRACTIONf_chiral_restr0.0552886
X-RAY DIFFRACTIONf_plane_restr0.0063210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.46780.33011390.26662563X-RAY DIFFRACTION75
2.4678-2.49680.35551470.272796X-RAY DIFFRACTION80
2.4968-2.52720.33621390.27232913X-RAY DIFFRACTION84
2.5272-2.55920.32131700.273128X-RAY DIFFRACTION90
2.5592-2.59290.35351630.27343190X-RAY DIFFRACTION92
2.5929-2.62840.36261510.27573269X-RAY DIFFRACTION94
2.6284-2.6660.33631820.25543388X-RAY DIFFRACTION96
2.666-2.70580.28111830.25763418X-RAY DIFFRACTION98
2.7058-2.74810.36261730.24933432X-RAY DIFFRACTION99
2.7481-2.79310.30611990.24283468X-RAY DIFFRACTION100
2.7931-2.84130.3131700.23813468X-RAY DIFFRACTION99
2.8413-2.8930.28021930.23063436X-RAY DIFFRACTION100
2.893-2.94860.29642000.22693474X-RAY DIFFRACTION100
2.9486-3.00880.31681820.22593502X-RAY DIFFRACTION100
3.0088-3.07420.30461770.22463461X-RAY DIFFRACTION99
3.0742-3.14570.30311770.23253485X-RAY DIFFRACTION100
3.1457-3.22440.28771900.22063464X-RAY DIFFRACTION100
3.2244-3.31160.29381940.21733487X-RAY DIFFRACTION100
3.3116-3.40910.24131910.20523466X-RAY DIFFRACTION100
3.4091-3.51910.25612000.19493449X-RAY DIFFRACTION100
3.5191-3.64490.25882080.18383474X-RAY DIFFRACTION100
3.6449-3.79080.22971890.17523469X-RAY DIFFRACTION100
3.7908-3.96330.21991880.16643509X-RAY DIFFRACTION100
3.9633-4.17230.2111700.1513517X-RAY DIFFRACTION100
4.1723-4.43370.19471780.14483476X-RAY DIFFRACTION100
4.4337-4.7760.16041770.13293527X-RAY DIFFRACTION100
4.776-5.25660.19621980.14873488X-RAY DIFFRACTION100
5.2566-6.01720.24541750.18193544X-RAY DIFFRACTION100
6.0172-7.58050.20591640.18513568X-RAY DIFFRACTION100
7.5805-95.17850.17111670.153626X-RAY DIFFRACTION100

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