[English] 日本語
Yorodumi
- PDB-9w2k: Structural basis of substrate promiscuity in the archaeal RNA-spl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9w2k
TitleStructural basis of substrate promiscuity in the archaeal RNA-splicing endonuclease from Candidatus Micrarchaeum acidiphilum (ARMAN-2)
Components
  • DNA/RNA (5'-R(P*AP*CP*CP*GP*AP*CP*CP*A)-D(P*U)-R(P*AP*GP*CP*U)-3')
  • RNA (5'-R(*AP*GP*GP*U)-3')
  • RNA (5'-R(P*AP*GP*CP*GP*GP*UP*CP*A)-3')
  • tRNA intron endonuclease
KeywordsSPLICING/RNA / Archaea / tRNA / Intron / Novel catalytic reaction / SPLICING / SPLICING-RNA complex
Function / homology
Function and homology information


tRNA-intron lyase activity / tRNA splicing, via endonucleolytic cleavage and ligation / nucleic acid binding / cytoplasm
Similarity search - Function
tRNA intron endonuclease, N-terminal domain superfamily / tRNA-splicing endonuclease / tRNA intron endonuclease, catalytic domain-like / tRNA intron endonuclease, catalytic C-terminal domain / tRNA intron endonuclease, catalytic domain-like superfamily / tRNA endonuclease-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE / ACETIC ACID / RNA / RNA (> 10) / tRNA intron endonuclease
Similarity search - Component
Biological speciesCandidatus Micrarchaeum acidiphilum ARMAN-2 (archaea)
Archaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsHirata, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K09352 Japan
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural basis of substrate diversity and functional evolution of archaeal RNA-splicing endonucleases.
Authors: Miyata, Y. / Yamagami, R. / Kawamura, T. / Hori, H. / Hirata, A.
History
DepositionJul 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA intron endonuclease
B: tRNA intron endonuclease
I: DNA/RNA (5'-R(P*AP*CP*CP*GP*AP*CP*CP*A)-D(P*U)-R(P*AP*GP*CP*U)-3')
F: RNA (5'-R(P*AP*GP*CP*GP*GP*UP*CP*A)-3')
H: RNA (5'-R(*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,34610
Polymers99,6965
Non-polymers6495
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-48 kcal/mol
Surface area34310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.514, 65.648, 71.802
Angle α, β, γ (deg.)114.462, 111.890, 90.010
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein tRNA intron endonuclease


Mass: 45882.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Micrarchaeum acidiphilum ARMAN-2 (archaea)
Gene: UNLARM2_0797 / Production host: Escherichia (bacteria) / References: UniProt: C7DIA5

-
RNA chain , 3 types, 3 molecules IFH

#2: RNA chain DNA/RNA (5'-R(P*AP*CP*CP*GP*AP*CP*CP*A)-D(P*U)-R(P*AP*GP*CP*U)-3')


Mass: 4084.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Archaeoglobus fulgidus (archaea)
#3: RNA chain RNA (5'-R(P*AP*GP*CP*GP*GP*UP*CP*A)-3')


Mass: 2565.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Archaeoglobus fulgidus (archaea)
#4: RNA chain RNA (5'-R(*AP*GP*GP*U)-3')


Mass: 1280.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Archaeoglobus fulgidus (archaea)

-
Non-polymers , 3 types, 354 molecules

#5: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-A23 / ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE


Type: RNA linking / Mass: 409.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O9P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.0M Ammonium sulfate, 0.1M Sodium acetate tri-hydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.798→50 Å / Num. obs: 73010 / % possible obs: 97.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 26.33
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.261 / Num. unique obs: 7189

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.798→33.529 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.97 / SU ML: 0.092 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.231 3707 5.077 %
Rwork0.1853 69302 -
all0.188 --
obs-73009 96.79 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.683 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å2-0.001 Å20.001 Å2
2---0.011 Å20.002 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 1.798→33.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 531 41 349 7209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127057
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166304
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.6619623
X-RAY DIFFRACTIONr_angle_other_deg0.5191.56614685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1465768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.1531054
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.852101198
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.15810301
X-RAY DIFFRACTIONr_chiral_restr0.0840.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027578
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021457
X-RAY DIFFRACTIONr_nbd_refined0.2340.21276
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.25896
X-RAY DIFFRACTIONr_nbtor_refined0.1880.23340
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23551
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2332
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.228
X-RAY DIFFRACTIONr_nbd_other0.2310.298
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.220
X-RAY DIFFRACTIONr_mcbond_it2.3532.2313082
X-RAY DIFFRACTIONr_mcbond_other2.3412.2293078
X-RAY DIFFRACTIONr_mcangle_it3.4333.3343844
X-RAY DIFFRACTIONr_mcangle_other3.4343.3343845
X-RAY DIFFRACTIONr_scbond_it3.0493.0013975
X-RAY DIFFRACTIONr_scbond_other3.0483.0013976
X-RAY DIFFRACTIONr_scangle_it4.6394.3845779
X-RAY DIFFRACTIONr_scangle_other4.6394.3845780
X-RAY DIFFRACTIONr_lrange_it6.73237.2688113
X-RAY DIFFRACTIONr_lrange_other6.72236.7128076
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.798-1.8450.2832410.2548390.25255410.9470.95991.68020.217
1.845-1.8950.2812550.21949650.22254390.9520.9795.97350.189
1.895-1.950.2572770.20447860.20752330.9550.97396.75140.173
1.95-2.010.2332490.19447040.19651320.9650.97796.51210.166
2.01-2.0750.2432620.19445650.19749860.9620.97696.81110.171
2.075-2.1480.2331980.17644530.17847930.9670.98197.03730.157
2.148-2.2290.2352300.17643310.17946920.9660.98197.2080.16
2.229-2.3190.2322290.17541210.17844690.9680.98197.33720.16
2.319-2.4220.2131910.17639540.17842660.9730.98197.16360.162
2.422-2.5390.2181900.1737740.17340760.970.98297.25220.159
2.539-2.6760.2361830.17536510.17839140.9640.98197.95610.167
2.676-2.8370.2131740.18234240.18336800.970.98197.77170.177
2.837-3.0310.2231720.17531840.17834520.9710.98197.2190.177
3.031-3.2720.2311700.17729970.1832460.9660.9897.56620.184
3.272-3.5810.2491750.18827050.19229520.9640.97897.5610.199
3.581-3.9980.21400.17224840.17326790.9790.98397.9470.19
3.998-4.6050.2021160.16722120.16923710.9770.98498.18640.193
4.605-5.6140.221200.18618740.18820130.9740.9899.05610.22
5.614-7.830.257950.22914660.23115700.9640.9799.42680.267
7.83-33.5290.284400.2178130.229050.9640.97194.25410.268

+
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