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- PDB-4bhq: Structure of the periplasmic domain of the PilN type IV pilus bio... -

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Basic information

Entry
Database: PDB / ID: 4bhq
TitleStructure of the periplasmic domain of the PilN type IV pilus biogenesis protein from Thermus thermophilus
ComponentsCOMPETENCE PROTEIN PILN
KeywordsCELL ADHESION / SECRETION
Function / homologyAlpha-Beta Plaits - #2830 / PilN biogenesis protein dimerization domain / PilN biogenesis protein dimerization domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Competence protein PilN
Function and homology information
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsKaruppiah, V. / Collins, R.F. / Gao, Y. / Thistlethwaite, A. / Derrick, J.P.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Structure and assembly of an inner membrane platform for initiation of type IV pilus biogenesis.
Authors: Vijaykumar Karuppiah / Richard F Collins / Angela Thistlethwaite / Ya Gao / Jeremy P Derrick /
Abstract: Type IV pili are long fibers that are assembled by polymerization of a major pilin protein in the periplasm of a wide range of bacteria and archaea. They play crucial roles in pathogenesis, DNA ...Type IV pili are long fibers that are assembled by polymerization of a major pilin protein in the periplasm of a wide range of bacteria and archaea. They play crucial roles in pathogenesis, DNA transformation, and motility, and are capable of rapid retraction, generating powerful motor forces. PilN and PilO are integral inner membrane proteins that are essential for type IV pilus formation. Here, we show that PilN and PilO from Thermus thermophilus can be isolated as a complex with PilM, a cytoplasmic protein with structural similarities to the cytoskeletal protein MreB. The crystal structure of the periplasmic portion of PilN forms a homodimer with an extensive, conserved interaction interface. We conducted serial 3D reconstructions by electron microscopy of PilMN, PilMNO, and PilMNO bound to the major pilin protein PilA4, to chart the assembly of the inner membrane pilus biogenesis platform. PilN drives the dimerization of the PilMN complex with a stoichiometry of 2:2; binding of two PilO monomers then causes the PilN periplasmic domains to dissociate. Finally, two PilA4 monomers bind to the periplasmic domains of PilN and PilO, to generate a T-shaped complex that is primed for addition of the pilin to the nascent pilus fiber. Docking of structures for PilM, PilN, PilO, and PilA4 into the electron density maps of the transmembrane complexes was used to generate a sequence of molecular structures that chart the initial events in type IV pilus formation, and provide structural information on the early events in this important secretion process.
History
DepositionApr 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMPETENCE PROTEIN PILN
B: COMPETENCE PROTEIN PILN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8833
Polymers35,8582
Non-polymers241
Water2,558142
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-36.9 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.830, 67.830, 147.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11B-2051-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (0.95, 0.31, 0.06), (0.31, -0.95), (0.06, 0.02, -1) / Vector: -10.35, 73.57, -36.52)

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Components

#1: Protein COMPETENCE PROTEIN PILN / PILN TYPE IV PILUS BIOGENESIS PROTEIN


Mass: 17929.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5SII9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCYTOPLASMIC AND TRANSMEMBRANE REGIONS REMOVED. THE FIRST FOUR RESIDUES (GSHM) AT THE N-TERMINUS AND ...CYTOPLASMIC AND TRANSMEMBRANE REGIONS REMOVED. THE FIRST FOUR RESIDUES (GSHM) AT THE N-TERMINUS AND THE LAST EIGHT RESIDUES (LEHHHHHH) ARE FROM THE EXPRESSION VECTOR

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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: 1.8 Å3/Da / Density % sol: 32 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M HEPES PH 7.0 0.2 M MAGNESIUM CHLORIDE 20% PEG 6000 10 MM ZINC CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 20669 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.9
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.4 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.05→47.96 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.6 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22623 1058 5.1 %RANDOM
Rwork0.19584 ---
obs0.19733 19607 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.416 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2--0.97 Å20 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 1 142 1831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9562307
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.36621.49487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70315279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.561526
X-RAY DIFFRACTIONr_chiral_restr0.1250.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211336
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 84 -
Rwork0.244 1405 -
obs--99 %

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