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- PDB-7sgp: Crystal structure of periplasmic domain of Helicobacter pylori Fl... -

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Basic information

Entry
Database: PDB / ID: 7sgp
TitleCrystal structure of periplasmic domain of Helicobacter pylori FliL (residues 81 to 183) (crystal form C)
ComponentsFlagellar protein FliL
KeywordsMOTOR PROTEIN / Flagellar motor / FliL
Function / homologyFlagellar basal body-associated protein FliL / Flagellar basal body-associated protein FliL / bacterial-type flagellum basal body / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane / Flagellar protein FliL
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.1 Å
AuthorsChan, K.L. / Peterson, B. / Khan, M.F. / Roujeinikova, A.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210103056 Australia
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: The flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation.
Authors: Shoichi Tachiyama / Kar L Chan / Xiaolin Liu / Skander Hathroubi / Briana Peterson / Mohammad F Khan / Karen M Ottemann / Jun Liu / Anna Roujeinikova /
Abstract: The flagellar motor stator is an ion channel nanomachine that assembles as a ring of the MotAMotB units at the flagellar base. The role of accessory proteins required for stator assembly and ...The flagellar motor stator is an ion channel nanomachine that assembles as a ring of the MotAMotB units at the flagellar base. The role of accessory proteins required for stator assembly and activation remains largely enigmatic. Here, we show that one such assembly factor, the conserved protein FliL, forms an integral part of the flagellar motor in a position that colocalizes with the stator. Cryogenic electron tomography reconstructions of the intact motor in whole wild-type cells and cells lacking FliL revealed that the periplasmic domain of FliL (FliL-C) forms 18 circumferentially positioned rings integrated with the 18 MotAB units. FliL-C formed partial rings in the crystal, and the crystal structure-based full ring model was consistent with the shape of the rings observed in situ. Our data suggest that each FliL ring is coaxially sandwiched between the MotA ring and the dimeric periplasmic MotB moiety of the stator unit and that the central hole of the FliL ring has density that is consistent with the plug/linker region of MotB in its extended, active conformation. Significant structural similarities were found between FliL-C and stomatin/prohibitin/flotillin/HflK/C domains of scaffolding proteins, suggesting that FliL acts as a scaffold. The binding energy released upon association of FliL with the stator units could be used to power the release of the plug helices. The finding that isolated FliL-C forms stable partial rings provides an insight into the putative mechanism by which the FliL rings assemble around the stator units.
History
DepositionOct 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar protein FliL


Theoretical massNumber of molelcules
Total (without water)12,6851
Polymers12,6851
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.513, 59.986, 60.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flagellar protein FliL


Mass: 12684.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fliL, BGL67_04255 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A293T1P9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium di-hydrogen phosphate, trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→42.76 Å / Num. obs: 9199 / % possible obs: 98.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.3 / Num. unique obs: 734

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.1→42.76 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.123 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 439 4.8 %RANDOM
Rwork0.1793 ---
obs0.1817 8723 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.34 Å2 / Biso mean: 43.704 Å2 / Biso min: 30.58 Å2
Baniso -1Baniso -2Baniso -3
1--2.32 Å20 Å20 Å2
2--1.87 Å20 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 2.1→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms808 0 0 61 869
Biso mean---54.73 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013825
X-RAY DIFFRACTIONr_bond_other_d0.0010.017819
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.6271113
X-RAY DIFFRACTIONr_angle_other_deg1.4181.5831908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2795103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01525.27836
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47715164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.045152
X-RAY DIFFRACTIONr_chiral_restr0.0820.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02899
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02151
LS refinement shellResolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 39 -
Rwork0.236 609 -
all-648 -
obs--98.18 %

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