[English] 日本語
Yorodumi
- PDB-8zig: Crystal structure of the methyltransferase PsiM in complex with s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zig
TitleCrystal structure of the methyltransferase PsiM in complex with s-adenosylmethionine (SAM)
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-ADENOSYLMETHIONINE / Psilocybin synthase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9522
Polymers34,5531
Non-polymers3981
Water3,603200
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 area13570 Å2
Unit cell
Length a, b, c (Å)58.339, 126.744, 39.559
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

#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 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-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000

-
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: 1.35→63.37 Å / Num. obs: 60331 / % possible obs: 93.1 % / Redundancy: 8.6 % / Biso Wilson estimate: 12.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.028 / Rrim(I) all: 0.084 / Net I/σ(I): 16.4
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5949 / CC1/2: 0.672 / Rpim(I) all: 0.307 / Rrim(I) all: 0.694 / % possible all: 64.2

-
Processing

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

8zie


Resolution: 1.35→31.7 Å / SU ML: 0.1239 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9837
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2038 3036 5.04 %
Rwork0.1825 57192 -
obs0.1836 60228 93.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17 Å2
Refinement stepCycle: LAST / Resolution: 1.35→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 27 200 2579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592470
X-RAY DIFFRACTIONf_angle_d1.02013367
X-RAY DIFFRACTIONf_chiral_restr0.0759381
X-RAY DIFFRACTIONf_plane_restr0.0123436
X-RAY DIFFRACTIONf_dihedral_angle_d6.9065352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.2844960.29061534X-RAY DIFFRACTION56.97
1.38-1.40.2803990.2691725X-RAY DIFFRACTION62.87
1.4-1.420.29711050.23281957X-RAY DIFFRACTION70.18
1.42-1.450.21361270.22392088X-RAY DIFFRACTION77.26
1.45-1.480.23681270.20822357X-RAY DIFFRACTION85.57
1.48-1.510.24011310.19662662X-RAY DIFFRACTION96.31
1.51-1.540.19581430.19262792X-RAY DIFFRACTION99.97
1.54-1.570.23981530.1842743X-RAY DIFFRACTION99.9
1.57-1.610.20451400.19242748X-RAY DIFFRACTION99.9
1.61-1.660.20931500.1862767X-RAY DIFFRACTION99.86
1.66-1.710.21381460.18352770X-RAY DIFFRACTION99.93
1.71-1.760.23411370.1892793X-RAY DIFFRACTION99.86
1.76-1.820.18721240.1872783X-RAY DIFFRACTION99.76
1.82-1.90.1791590.17962771X-RAY DIFFRACTION99.69
1.9-1.980.22821490.18282757X-RAY DIFFRACTION99.08
1.98-2.090.18331470.18512811X-RAY DIFFRACTION99.8
2.09-2.220.19271480.17912780X-RAY DIFFRACTION99.8
2.22-2.390.18051390.18142786X-RAY DIFFRACTION99.42
2.39-2.630.25371460.18882851X-RAY DIFFRACTION99.83
2.63-3.010.21541620.18942811X-RAY DIFFRACTION99.93
3.01-3.790.19041550.17232875X-RAY DIFFRACTION99.87
3.79-31.70.17581530.16063031X-RAY DIFFRACTION99.72
Refinement TLS params.Method: refined / Origin x: -16.7414360052 Å / Origin y: 15.6947350832 Å / Origin z: -16.4189349989 Å
111213212223313233
T0.083735671269 Å2-0.00603755520643 Å20.0075401850385 Å2-0.0839572075444 Å20.00309387188579 Å2--0.0857081270154 Å2
L0.630120790234 °2-0.0121845123435 °20.150135461621 °2-0.696499948806 °2-0.0496243280525 °2--0.722538842305 °2
S-0.00545176855619 Å °-0.00398913462848 Å °0.0385217180973 Å °0.000768247806298 Å °-0.00898392015628 Å °-0.0434349684488 Å °-0.0228610164825 Å °0.0462943968689 Å °0.0143626262272 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more