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- PDB-8zio: Crystal structure of the methyltransferase PsiM in complex with S... -

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Basic information

Entry
Database: PDB / ID: 8zio
TitleCrystal structure of the methyltransferase PsiM in complex with SAH and Psilocybin
ComponentsPsilocybin synthase
KeywordsTRANSFERASE / norbaeocystin / baeocystin / psilocybin / methyltransferase / SAM / SAH
Function / homology
Function and homology information


psilocybin synthase / 4-hydroxytryptamine 4-phosphate methyltransferase activity / psilocybin biosynthetic process / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases / nucleus
Similarity search - Function
Methyltransferase METTL16/PsiM / RNA methyltransferase / METTL16/RlmF family / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / : / Psilocybin synthase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMeng, C.Y. / Wen, Y. / Guo, W.T. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for psilocybin biosynthesis.
Authors: Meng, C. / Guo, W. / Xiao, C. / Wen, Y. / Zhu, X. / Zhang, Q. / Liang, Y. / Li, H. / Xu, S. / Qiu, Y. / Chen, H. / Lin, W.J. / Wu, B.
History
DepositionMay 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3144
Polymers34,5531
Non-polymers7613
Water8,431468
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint0 kcal/mol
Surface area13430 Å2
Unit cell
Length a, b, c (Å)39.410, 56.480, 131.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Psilocybin synthase / Psilocybin biosynthesis methyltransferase


Mass: 34553.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SAH is ligand / Source: (gene. exp.) Psilocybe cubensis (magic mushroom) / Gene: psiM / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DPA9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-X8Q / Psilocybin / [3-[2-(dimethylamino)ethyl]-1~{H}-indol-4-yl] dihydrogen phosphate


Mass: 284.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N2O4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium acetate, 0.1 M Sodium cacodylate pH 6.5, 30% w/v PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 53061 / % possible obs: 99.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 9.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.035 / Rrim(I) all: 0.121 / Net I/σ(I): 18
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2548 / CC1/2: 0.752 / Rpim(I) all: 0.351 / Rrim(I) all: 0.869 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ZIE

8zie


Resolution: 1.45→29.33 Å / SU ML: 0.1305 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.6109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1819 2707 5.11 %
Rwork0.1611 50287 -
obs0.1622 52994 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.91 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 25 468 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00492564
X-RAY DIFFRACTIONf_angle_d0.82593495
X-RAY DIFFRACTIONf_chiral_restr0.0706388
X-RAY DIFFRACTIONf_plane_restr0.0087451
X-RAY DIFFRACTIONf_dihedral_angle_d14.5811938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.29571500.23942540X-RAY DIFFRACTION98.28
1.48-1.50.20331490.19922576X-RAY DIFFRACTION99.56
1.5-1.540.25151410.21132618X-RAY DIFFRACTION99.57
1.54-1.570.18621450.16562626X-RAY DIFFRACTION100
1.57-1.610.18791350.16072582X-RAY DIFFRACTION100
1.61-1.650.20911360.16052653X-RAY DIFFRACTION100
1.65-1.690.17891440.16032594X-RAY DIFFRACTION100
1.69-1.740.1991360.15742623X-RAY DIFFRACTION100
1.74-1.80.1631370.15632656X-RAY DIFFRACTION100
1.8-1.860.18671550.16152620X-RAY DIFFRACTION100
1.86-1.930.18761310.1732624X-RAY DIFFRACTION99.78
1.93-2.020.18251560.15632655X-RAY DIFFRACTION100
2.02-2.130.18291320.15892605X-RAY DIFFRACTION99.89
2.13-2.260.20151510.15262660X-RAY DIFFRACTION99.75
2.26-2.440.20111550.16182661X-RAY DIFFRACTION100
2.44-2.680.18451420.16292664X-RAY DIFFRACTION99.96
2.68-3.070.15971460.16172696X-RAY DIFFRACTION100
3.07-3.870.14641160.14762768X-RAY DIFFRACTION100
3.87-29.330.15681500.15012866X-RAY DIFFRACTION99.87

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