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- PDB-7o76: Reversible supramolecular assembly of the anti-microbial peptide ... -

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Basic information

Entry
Database: PDB / ID: 7o76
TitleReversible supramolecular assembly of the anti-microbial peptide plectasin
ComponentsFungal defensin plectasin
KeywordsANTIMICROBIAL PROTEIN / fungal defensin
Function / homology
Function and homology information


potassium channel regulator activity / toxin activity / defense response to bacterium / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Arthropod defensin / Invertebrate defensins family profile. / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Fungal defensin plectasin
Similarity search - Component
Biological speciesPseudoplectania nigrella (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.131 Å
AuthorsPohl, C. / Noergaard, N. / Harris, P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675074European Union
CitationJournal: Nat Commun / Year: 2022
Title: pH- and concentration-dependent supramolecular assembly of a fungal defensin plectasin variant into helical non-amyloid fibrils.
Authors: Christin Pohl / Gregory Effantin / Eaazhisai Kandiah / Sebastian Meier / Guanghong Zeng / Werner Streicher / Dorotea Raventos Segura / Per H Mygind / Dorthe Sandvang / Line Anker Nielsen / ...Authors: Christin Pohl / Gregory Effantin / Eaazhisai Kandiah / Sebastian Meier / Guanghong Zeng / Werner Streicher / Dorotea Raventos Segura / Per H Mygind / Dorthe Sandvang / Line Anker Nielsen / Günther H J Peters / Guy Schoehn / Christoph Mueller-Dieckmann / Allan Noergaard / Pernille Harris /
Abstract: Self-assembly and fibril formation play important roles in protein behaviour. Amyloid fibril formation is well-studied due to its role in neurodegenerative diseases and characterized by refolding of ...Self-assembly and fibril formation play important roles in protein behaviour. Amyloid fibril formation is well-studied due to its role in neurodegenerative diseases and characterized by refolding of the protein into predominantly β-sheet form. However, much less is known about the assembly of proteins into other types of supramolecular structures. Using cryo-electron microscopy at a resolution of 1.97 Å, we show that a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembles into helical non-amyloid fibrils. The in vitro anti-microbial activity was determined and shown to be enhanced compared to the wildtype. Plectasin contains a cysteine-stabilised α-helix-β-sheet structure, which remains intact upon fibril formation. Two protofilaments form a right-handed protein fibril. The fibril formation is reversible and follows sigmoidal kinetics with a pH- and concentration dependent equilibrium between soluble monomer and protein fibril. This high-resolution structure reveals that α/β proteins can natively assemble into fibrils.
History
DepositionApr 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
XXX: Fungal defensin plectasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5212
Polymers4,4151
Non-polymers1061
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint1 kcal/mol
Surface area2920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.678, 20.093, 32.546
Angle α, β, γ (deg.)90.000, 104.279, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Fungal defensin plectasin


Mass: 4415.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoplectania nigrella (fungus) / Gene: DEF / Production host: Aspergillus oryzae (mold) / References: UniProt: Q53I06
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.7 Å3/Da / Density % sol: 27.62 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 15 mg/mL plectasin in 10 mM His pH 4.5 added to a reservoir of 0.1 M NH4Ac, 0.1 M Tris pH 8.5 and 40% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97247 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2020 / Details: Kirkpatrick-Baez (KB) mirror pair (VFM, HFM)
RadiationMonochromator: Si (111), double crystal monochromator, horizontally deflecting, LN2 side-cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97247 Å / Relative weight: 1
ReflectionResolution: 1.13→31.53 Å / Num. obs: 10216 / % possible obs: 89.9 % / Redundancy: 6 % / CC1/2: 0.999 / Net I/σ(I): 22.49
Reflection shellResolution: 1.13→1.2 Å / Num. unique obs: 1020 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E7U

3e7u


Resolution: 1.131→21.219 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.164 / SU B: 2.377 / SU ML: 0.045 / Average fsc free: 0.9365 / Average fsc work: 0.9497 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.04
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1781 507 4.963 %
Rwork0.1457 9708 -
all0.147 --
obs-10215 90.231 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.922 Å2
Baniso -1Baniso -2Baniso -3
1-2.945 Å2-0 Å21.224 Å2
2---2.283 Å2-0 Å2
3----1.137 Å2
Refinement stepCycle: LAST / Resolution: 1.131→21.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms305 0 7 24 336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.012342
X-RAY DIFFRACTIONr_bond_other_d0.0040.018280
X-RAY DIFFRACTIONr_angle_refined_deg1.9651.639457
X-RAY DIFFRACTIONr_angle_other_deg0.6861.606658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.441543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95524.37516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.9521555
X-RAY DIFFRACTIONr_chiral_restr0.0950.235
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02403
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0281
X-RAY DIFFRACTIONr_nbd_refined0.2520.269
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2440.2255
X-RAY DIFFRACTIONr_nbtor_refined0.2080.2160
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0980.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2610.212
X-RAY DIFFRACTIONr_nbd_other0.2550.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.214
X-RAY DIFFRACTIONr_mcbond_it2.6672.271166
X-RAY DIFFRACTIONr_mcbond_other2.6712.27165
X-RAY DIFFRACTIONr_mcangle_it3.4143.427208
X-RAY DIFFRACTIONr_mcangle_other3.4063.427209
X-RAY DIFFRACTIONr_scbond_it7.272.931176
X-RAY DIFFRACTIONr_scbond_other7.0052.895170
X-RAY DIFFRACTIONr_scangle_it7.734.143248
X-RAY DIFFRACTIONr_scangle_other7.4954.105243
X-RAY DIFFRACTIONr_lrange_it7.75128.877388
X-RAY DIFFRACTIONr_lrange_other6.99427.986381
X-RAY DIFFRACTIONr_rigid_bond_restr6.4383622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.131-1.160.398180.385341X-RAY DIFFRACTION43.3575
1.16-1.1920.321250.302495X-RAY DIFFRACTION64.0394
1.192-1.2270.223360.25572X-RAY DIFFRACTION78.2497
1.227-1.2640.278390.216638X-RAY DIFFRACTION88.3812
1.264-1.3060.176290.181705X-RAY DIFFRACTION98.9218
1.306-1.3510.198350.177686X-RAY DIFFRACTION99.8615
1.351-1.4020.21360.161645X-RAY DIFFRACTION100
1.402-1.4590.15270.148630X-RAY DIFFRACTION99.848
1.459-1.5240.181260.149611X-RAY DIFFRACTION99.8433
1.524-1.5980.195300.129591X-RAY DIFFRACTION99.679
1.598-1.6850.193260.123561X-RAY DIFFRACTION99.8299
1.685-1.7870.174300.132516X-RAY DIFFRACTION100
1.787-1.9090.241210.122500X-RAY DIFFRACTION100
1.909-2.0620.196270.125460X-RAY DIFFRACTION99.1853
2.062-2.2580.199230.124419X-RAY DIFFRACTION98.6607
2.258-2.5230.136210.133387X-RAY DIFFRACTION99.7555
2.523-2.910.203250.141342X-RAY DIFFRACTION99.458
2.91-3.5560.213130.147292X-RAY DIFFRACTION99.3485
3.556-4.9970.111150.137210X-RAY DIFFRACTION90.7258
4.997-100.20550.254107X-RAY DIFFRACTION76.1905

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