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

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Basic information

Entry
Database: PDB / ID: 8zii
TitleCrystal structure of the methyltransferase PsiM in complex with SAH and Norbaeocystin
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: 2.5 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)35,1943
Polymers34,5531
Non-polymers6412
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.422, 57.530, 129.465
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: The first residue is from 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: Chemical ChemComp-XP6 / Norbaeocystin / [3-(2-azanylethyl)-1~{H}-indol-4-yl] dihydrogen phosphate


Mass: 256.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N2O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 40% (v/v) Isopropanol,0.1M Imidazole/Hydrochloric acid pH 6.5, 15% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 10761 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 26.97 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.054 / Rrim(I) all: 0.194 / Net I/σ(I): 10.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1527 / CC1/2: 0.964 / Rpim(I) all: 0.154 / Rrim(I) all: 0.553 / % possible all: 100

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Processing

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

8zie


Resolution: 2.5→29.11 Å / SU ML: 0.1902 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4649
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2173 512 4.77 %
Rwork0.1736 10211 -
obs0.1759 10723 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.61 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 43 113 2584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782543
X-RAY DIFFRACTIONf_angle_d0.9913465
X-RAY DIFFRACTIONf_chiral_restr0.054386
X-RAY DIFFRACTIONf_plane_restr0.0135447
X-RAY DIFFRACTIONf_dihedral_angle_d8.6148362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.24781060.22498X-RAY DIFFRACTION99.88
2.75-3.150.28441290.20592501X-RAY DIFFRACTION99.96
3.15-3.970.24341430.16822531X-RAY DIFFRACTION100
3.97-29.110.15481340.15252681X-RAY DIFFRACTION99.96

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