[English] 日本語
Yorodumi
- PDB-9s1d: Crystal structure of the methyltransferase ribozyme 1 with two 2'... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9s1d
TitleCrystal structure of the methyltransferase ribozyme 1 with two 2'O-methylation (MTR1m2)
Components
  • Chains: A
  • Chains: B
  • Chains: C
KeywordsRNA / Ribozyme / methyltransferase / 2'O-methylation / accelerated catalysis
Function / homologyGUANINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, H.-A. / Scheitl, C.P.M. / Hoebartner, C.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Research Council (ERC)European Union
Citation
Journal: Nat Commun / Year: 2026
Title: A magic methyl effect in the active site of a methyltransferase ribozyme.
Authors: Aupic, J. / Chen, H.A. / Scheitl, C.P.M. / Hobartner, C. / Magistrato, A.
#1: Journal: Nat Chem Biol / Year: 2022
Title: Structure and mechanism of the methyltransferase ribozyme MTR1.
Authors: Scheitl, C.P.M. / Mieczkowski, M. / Schindelin, H. / Hoebartner, C.
History
DepositionJul 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2026Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chains: A
B: Chains: B
C: Chains: C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1088
Polymers19,8623
Non-polymers2465
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Dissolved crystals were injected into anion exchange HPLC to check the composition. Peak areas were integrated to calculate the ratio of the RNA species.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-20 kcal/mol
Surface area9610 Å2
Unit cell
Length a, b, c (Å)71.323, 71.323, 83.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

-
RNA chain , 3 types, 3 molecules ABC

#1: RNA chain Chains: A


Mass: 4436.710 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized RNA oligonucleotide. N1-methylation of A7 occurred during crystallization process.
Source: (synth.) synthetic construct (others)
#2: RNA chain Chains: B


Mass: 7655.662 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized RNA oligonucleotide. 2'O-methyl modification at position 12 was introduced during solid-phase synthesis.
Source: (synth.) synthetic construct (others)
#3: RNA chain Chains: C


Mass: 7769.729 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized RNA oligonucleotide. 2'O-methyl modification at position 42 was introduced during solid-phase synthesis.
Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 50 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 67.16 % / Description: 50-150 um short rod
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 uM RNA in a ratio of A:B:C=1:1:1 in 10 mM HEPES pH7.5, 50 mM potassium chloride, 5 mM magnesium chloride and 240 uM of O6-methylguanine Crystallization cocktail: 100 mM NaCl, 100 mM ...Details: 200 uM RNA in a ratio of A:B:C=1:1:1 in 10 mM HEPES pH7.5, 50 mM potassium chloride, 5 mM magnesium chloride and 240 uM of O6-methylguanine Crystallization cocktail: 100 mM NaCl, 100 mM LiCl, 10 mM MgCl2, 50 mM MES pH 6.4-6.7, 36-42% MPD
PH range: 6.4-6.7 / Temp details: Growth in a thermally controlled cabinet

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cold nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 6, 2021
RadiationMonochromator: Si-111 and Si-113 reflection / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→43.17 Å / Num. obs: 7084 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 25.3 % / Biso Wilson estimate: 76.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.01 / Rrim(I) all: 0.045 / Χ2: 1.04 / Net I/σ(I): 42.9
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 27 % / Rmerge(I) obs: 2.017 / Mean I/σ(I) obs: 2 / Num. unique obs: 837 / CC1/2: 0.583 / Rpim(I) all: 0.396 / Rrim(I) all: 2.039 / Χ2: 0.82 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSJune 30 2024data reduction
PHASER2.8.3phasing
Coot0.9.8.95model building
PHENIX1.21.2_5419refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→43.17 Å / SU ML: 0.3643 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.8536
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Hendrickson-Lattman coefficients were generated in Phenix Resolve based on a non-methylated 7Q7X model, which was used in Phenix Refine as phase restraints (target function: MLHL). Three ...Details: Hendrickson-Lattman coefficients were generated in Phenix Resolve based on a non-methylated 7Q7X model, which was used in Phenix Refine as phase restraints (target function: MLHL). Three methyl groups were introduced during following refinements according to the difference map peaks.
RfactorNum. reflection% reflection
Rfree0.251 347 4.92 %
Rwork0.2201 6700 -
obs0.2216 7047 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1314 15 45 1374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531479
X-RAY DIFFRACTIONf_angle_d0.93982297
X-RAY DIFFRACTIONf_chiral_restr0.0357304
X-RAY DIFFRACTIONf_plane_restr0.004963
X-RAY DIFFRACTIONf_dihedral_angle_d24.5219916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.980.37421070.35042181X-RAY DIFFRACTION100
2.98-3.750.28311190.22592195X-RAY DIFFRACTION99.96
3.75-43.170.18221210.16532324X-RAY DIFFRACTION99.92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.596419922441.675457696640.9604917295523.564519315841.171731732590.7455357228090.1184553556640.260724882017-0.311627276199-0.2377317437790.0356448061689-0.08839430668260.29230064591-0.09009638335930.1100184293310.318956045333-0.0748165062825-0.01513365751230.202307585073-0.06364902729730.24783793968529.1686159186-16.3828363238-2.89113323894
20.6741855219930.3676963637150.6327056898161.08691547608-0.1545365263210.8765159242610.117291887635-0.4519435587840.2950511603130.313676254785-0.1265348522870.157439083876-0.151977470763-0.3865443287620.3902291715060.553361452507-0.126562964573-0.0320744548710.536193803645-0.2896370925220.46980569082715.0520399238-17.44117652831.45283493938
31.628179182640.582923080757-0.3711573495451.577620071810.2922174360491.325559739580.380601500117-0.1960166345930.158105586640.145792293277-0.3323951116350.200929723535-0.0927214020278-0.3500104063660.3131919198240.174227088256-0.0680527587317-0.0311957077180.227114154838-0.03770526456270.19679616929328.7370251761-6.791536443283.31715974388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'C' and resid 25 through 101)CC25 - 48
2X-RAY DIFFRACTION2(chain 'A' and resid 1 through 14)AA1 - 14
3X-RAY DIFFRACTION3(chain 'B' and resid 1 through 24)BB1 - 24

+
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