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- PDB-5aof: Crystal structure of pneumolysin deletion mutant Delta146_147. -

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Basic information

Entry
Database: PDB / ID: 5aof
TitleCrystal structure of pneumolysin deletion mutant Delta146_147.
ComponentsPNEUMOLYSIN
KeywordsTOXIN / CHOLESTEROL DEPENDENT CYTOLYSIN / PORE FORMING TOXIN
Function / homology
Function and homology information


cholesterol binding / toxin activity / killing of cells of another organism / host cell plasma membrane / extracellular region / membrane / cytoplasm
Similarity search - Function
Perfringolysin, domain 4 / Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / Immunoglobulin-like ...Perfringolysin, domain 4 / Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pneumolysin / Pneumolysin
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
Authorsvan Pee, K. / Yildiz, O.
CitationJournal: Elife / Year: 2017
Title: CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin.
Authors: Katharina van Pee / Alexander Neuhaus / Edoardo D'Imprima / Deryck J Mills / Werner Kühlbrandt / Özkan Yildiz /
Abstract: Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of ...Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of , by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel. The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the inner barrel surface is highly charged. Comparison of the cryoEM pore complex to the prepore structure obtained by electron cryo-tomography and the x-ray structure of the soluble form reveals the detailed mechanisms by which the toxin monomers insert into the lipid bilayer to perforate the target membrane.
History
DepositionSep 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PNEUMOLYSIN


Theoretical massNumber of molelcules
Total (without water)54,7081
Polymers54,7081
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.730, 163.500, 207.800
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 PNEUMOLYSIN / THIOL-ACTIVATED CYTOLYSIN / CHOLESTEROL DEPENDENT CYTOLYSIN


Mass: 54708.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q04IN8, UniProt: Q7ZAK5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES AT THE POSITION 146 AND 147 DELETED.

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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: 3.84 Å3/Da / Density % sol: 67.96 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97798
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97798 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 29724 / % possible obs: 91 % / Observed criterion σ(I): 1.3 / Redundancy: 4.6 % / Biso Wilson estimate: 45.02 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.07
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 4.47 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.3 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AOD

5aod


Resolution: 2.45→48.263 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1486 5 %
Rwork0.2081 --
obs0.2094 29719 91.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→48.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 0 152 4008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023937
X-RAY DIFFRACTIONf_angle_d0.6465352
X-RAY DIFFRACTIONf_dihedral_angle_d15.0171438
X-RAY DIFFRACTIONf_chiral_restr0.024607
X-RAY DIFFRACTIONf_plane_restr0.002692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.52910.34611350.33212548X-RAY DIFFRACTION94
2.5291-2.61950.33031330.30682534X-RAY DIFFRACTION93
2.6195-2.72430.33771370.29132611X-RAY DIFFRACTION92
2.7243-2.84830.31951340.28792538X-RAY DIFFRACTION93
2.8483-2.99850.29411330.25122519X-RAY DIFFRACTION91
2.9985-3.18630.25531350.23372582X-RAY DIFFRACTION92
3.1863-3.43230.23021350.21312548X-RAY DIFFRACTION91
3.4323-3.77750.22371330.19792536X-RAY DIFFRACTION91
3.7775-4.32380.19061340.17222555X-RAY DIFFRACTION89
4.3238-5.44640.17831370.15312584X-RAY DIFFRACTION89
5.4464-48.27260.2121400.18412678X-RAY DIFFRACTION86
Refinement TLS params.Method: refined / Origin x: 27.2898 Å / Origin y: 326.2358 Å / Origin z: 466.6321 Å
111213212223313233
T0.3712 Å2-0.0028 Å2-0.0004 Å2-0.3902 Å2-0.0795 Å2--0.3521 Å2
L-0.0718 °20.2915 °20.3918 °2-1.3656 °22.0978 °2--2.3864 °2
S0.0801 Å °-0.0351 Å °-0.0147 Å °-0.0055 Å °-0.0269 Å °-0.0622 Å °0.065 Å °-0.1572 Å °-0.0391 Å °
Refinement TLS groupSelection details: ALL

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