[English] 日本語
Yorodumi
- PDB-1r3e: Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1r3e
TitleCrystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit
Components
  • 5'-R(*CP*UP*GP*UP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'
  • 5'-R(*CP*UP*GP*UP*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'
  • tRNA pseudouridine synthase B
KeywordsLYASE/RNA / RNA modification / pseudouridylation / LYASE-RNA COMPLEX
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / tRNA pseudouridine(55) synthase activity / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / RNA binding
Similarity search - Function
tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase / tRNA pseudouridylate synthase B, C-terminal / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase II, N-terminal / TruB family pseudouridylate synthase (N terminal domain) / PUA domain / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 ...tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase / tRNA pseudouridylate synthase B, C-terminal / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase II, N-terminal / TruB family pseudouridylate synthase (N terminal domain) / PUA domain / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Pseudouridine synthase, catalytic domain superfamily / PUA domain / PUA domain superfamily / PUA domain profile. / PUA-like superfamily / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA pseudouridine synthase B
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsPan, H. / Agarwalla, S. / Moustakas, D.T. / Finer-Moore, J. / Stroud, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA Recognition Through a Combination of Rigid Docking and Induced Fit
Authors: Pan, H. / Agarwalla, S. / Moustakas, D.T. / Finer-Moore, J. / Stroud, R.M.
History
DepositionOct 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_validate_close_contact
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp ..._exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-R(*CP*UP*GP*UP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'
D: 5'-R(*CP*UP*GP*UP*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'
E: 5'-R(*CP*UP*GP*UP*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'
A: tRNA pseudouridine synthase B


Theoretical massNumber of molelcules
Total (without water)51,6934
Polymers51,6934
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.862, 159.337, 44.545
Angle α, β, γ (deg.)90.00, 97.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-386-

HOH

21A-494-

HOH

-
Components

#1: RNA chain 5'-R(*CP*UP*GP*UP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'


Mass: 5416.227 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*CP*UP*GP*UP*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'


Mass: 5380.221 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein tRNA pseudouridine synthase B / EC 4.2.1.70 / tRNA pseudouridine 55 synthase / Psi55 synthase / Pseudouridylate synthase / Uracil hydrolyase


Mass: 35516.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TRUB / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q9WZW0, pseudouridylate synthase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.41 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, magnesium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2magnesium sulfate11
3sodium cacodylate11
4H2O11
5ammonium sulfate12
6magnesium sulfate12
7sodium cacodylate12
8H2O12
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 mg/mlprotein1drop
210 mMTris1droppH7.5
32 mMEDTA1drop
42 mMdithiothreitol1drop
51.9 M1reservoir
65 mM1reservoirMgCl2
7100 mM1reservoirpH6.5
81

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9730, 0.9796, 0.9800, 1.1271
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2002 / Details: mirrors
RadiationMonochromator: Double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9731
20.97961
30.981
41.12711
ReflectionResolution: 2.1→15 Å / Num. all: 39270 / Num. obs: 38642 / % possible obs: 98.4 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.18 Å / % possible all: 97.5
Reflection
*PLUS
Num. measured all: 525236
Reflection shell
*PLUS
% possible obs: 97.5 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 45.3

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→15 Å / σ(F): 2.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1159 -RANDOM
Rwork0.223 ---
obs0.223 38642 98.4 %-
all-39270 --
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 1067 0 263 3789
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_angle_deg1.36
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å / Num. reflection obs: 34732
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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