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- PDB-4bhr: Structure of the TTHA1221 type IV pilin protein from Thermus ther... -

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Basic information

Entry
Database: PDB / ID: 4bhr
TitleStructure of the TTHA1221 type IV pilin protein from Thermus thermophilus
ComponentsPILIN, TYPE IV
KeywordsCELL ADHESION / SECRETION
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #70 / Pilin A4 / Pilin A4 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Pilin, type IV, putative
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PILIN, TYPE IV
B: PILIN, TYPE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3663
Polymers20,2702
Non-polymers961
Water2,396133
1
A: PILIN, TYPE IV


Theoretical massNumber of molelcules
Total (without water)10,1351
Polymers10,1351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PILIN, TYPE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2312
Polymers10,1351
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.790, 36.790, 207.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.32, -0.95), (-0.13, -0.94, 0.31), (-0.99, 0.12, -0.05)
Vector: 24, -38.36, -2.2)

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Components

#1: Protein PILIN, TYPE IV /


Mass: 10134.958 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5SIZ3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL REGION REMOVED BY CLONING AND REPLACED WITH PELB LEADER SEQUENCE, WHICH WILL BE CLEAVED ...N-TERMINAL REGION REMOVED BY CLONING AND REPLACED WITH PELB LEADER SEQUENCE, WHICH WILL BE CLEAVED ON EXPORT TO THE PERIPLASM

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7
Details: 150 MM MOPS PH 7.0, 6.0 % V/V ETHYLENE GLYCOL, 1.8 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.946
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. obs: 19190 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.1
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.5 / % possible all: 99.6

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Processing

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

Resolution: 1.7→69.27 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.408 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24079 959 5.1 %RANDOM
Rwork0.21605 ---
obs0.21728 17721 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.559 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→69.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 5 133 1361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021250
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9231718
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.175165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61125.93259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80415157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.839155
X-RAY DIFFRACTIONr_chiral_restr0.1170.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021987
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 63 -
Rwork0.26 1071 -
obs--91.23 %

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