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- PDB-8zih: Crystal structure of the methyltransferase PsiM in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 8zih
TitleCrystal structure of the methyltransferase PsiM in complex with SAH
ComponentsPsilocybin synthase
KeywordsTRANSFERASE / norbaeocystin / baeocystin / psilocybin / methyltransferase / SAM
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: 1.31 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)34,9382
Polymers34,5531
Non-polymers3841
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13680 Å2
Unit cell
Length a, b, c (Å)56.351, 134.479, 39.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-842-

HOH

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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: The first serine residue is from the tag / 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


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


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.2 M Potassium phosphate (dibasic)/0.8M Sodium phosphate (monobasic), 0.1M Sodium acetate/Acetic acid pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.31→51.79 Å / Num. obs: 67276 / % possible obs: 92.1 % / Redundancy: 8.7 % / Biso Wilson estimate: 10.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.022 / Rrim(I) all: 0.068 / Net I/σ(I): 19.5
Reflection shellResolution: 1.31→1.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 6412 / CC1/2: 0.836 / Rpim(I) all: 0.211 / Rrim(I) all: 0.407 / % possible all: 62.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ZIE

8zie


Resolution: 1.31→32.36 Å / SU ML: 0.1086 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4739
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1849 3368 5.01 %
Rwork0.1657 63808 -
obs0.1667 67176 91.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.42 Å2
Refinement stepCycle: LAST / Resolution: 1.31→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 26 376 2830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592550
X-RAY DIFFRACTIONf_angle_d1.0363478
X-RAY DIFFRACTIONf_chiral_restr0.0763390
X-RAY DIFFRACTIONf_plane_restr0.0101453
X-RAY DIFFRACTIONf_dihedral_angle_d6.7779364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.330.2666890.23831486X-RAY DIFFRACTION52.66
1.33-1.350.2584830.20631726X-RAY DIFFRACTION59.7
1.35-1.370.205820.1891869X-RAY DIFFRACTION64.8
1.37-1.390.23071140.1822056X-RAY DIFFRACTION72.75
1.39-1.420.20841340.1812233X-RAY DIFFRACTION77.76
1.42-1.440.20721350.17712402X-RAY DIFFRACTION84.93
1.44-1.470.20271420.16772673X-RAY DIFFRACTION92.63
1.47-1.50.20761530.16652781X-RAY DIFFRACTION98.29
1.5-1.530.17581680.15852860X-RAY DIFFRACTION99.51
1.53-1.570.20171480.15492871X-RAY DIFFRACTION99.77
1.57-1.610.18381510.15162861X-RAY DIFFRACTION99.87
1.61-1.650.16651470.15352894X-RAY DIFFRACTION99.8
1.65-1.70.17731490.15022849X-RAY DIFFRACTION100
1.7-1.750.2151510.16482881X-RAY DIFFRACTION99.97
1.75-1.820.19271680.1772887X-RAY DIFFRACTION99.97
1.82-1.890.16961320.16392921X-RAY DIFFRACTION100
1.89-1.970.20711480.18582885X-RAY DIFFRACTION99.18
1.97-2.080.18221380.16332902X-RAY DIFFRACTION100
2.08-2.210.18951460.1622916X-RAY DIFFRACTION99.87
2.21-2.380.18641670.17832849X-RAY DIFFRACTION98.59
2.38-2.620.19541630.16962928X-RAY DIFFRACTION99.77
2.62-30.20681320.17642980X-RAY DIFFRACTION99.74
3-3.780.16851550.15642975X-RAY DIFFRACTION99.59
3.78-32.360.15151730.15223123X-RAY DIFFRACTION99.52
Refinement TLS params.Method: refined / Origin x: 12.2908614885 Å / Origin y: 17.2777696281 Å / Origin z: 3.24125873917 Å
111213212223313233
T0.0475897250408 Å2-0.000834557858497 Å20.00319127852239 Å2-0.0455671694266 Å20.000471381528407 Å2--0.0471136514128 Å2
L0.273117244956 °2-0.0783611926295 °20.0678510052712 °2-0.186389598155 °2-0.060745772871 °2--0.282363341624 °2
S0.00152107122397 Å °0.00468551207187 Å °0.0152777945861 Å °-0.0171006125106 Å °-0.0134513566836 Å °-0.0015061527374 Å °0.0169810617502 Å °0.0207381340006 Å °3.80196445622E-6 Å °
Refinement TLS groupSelection details: all

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