[English] 日本語
Yorodumi
- PDB-1ze2: Conformational change of pseudouridine 55 synthase upon its assoc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ze2
TitleConformational change of pseudouridine 55 synthase upon its association with RNA substrate
Components
  • 5'-R(*GP*GP*CP*CP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*AP*UP*CP*CP*GP*UP*GP*GP*C)-3'
  • tRNA pseudouridine synthase B
KeywordsLYASE/RNA / Protein-RNA complex / LYASE-RNA COMPLEX
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / mRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / RNA binding
Similarity search - Function
tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain / PUA domain / Pseudouridine synthase, catalytic domain superfamily ...tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA domain / PUA domain profile. / PUA domain superfamily / 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: 3 Å
AuthorsPhannachet, K. / Huang, R.H.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Conformational change of pseudouridine 55 synthase upon its association with RNA substrate
Authors: Phannachet, K. / Huang, R.H.
History
DepositionApr 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE According to the authors the conflicts at residues 296 and 307 are likely due to an error ...SEQUENCE According to the authors the conflicts at residues 296 and 307 are likely due to an error in the database sequence.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,2914
Polymers85,2914
Non-polymers00
Water3,387188
1
C: 5'-R(*GP*GP*CP*CP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*AP*UP*CP*CP*GP*UP*GP*GP*C)-3'
A: tRNA pseudouridine synthase B


Theoretical massNumber of molelcules
Total (without water)42,6452
Polymers42,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-R(*GP*GP*CP*CP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*AP*UP*CP*CP*GP*UP*GP*GP*C)-3'
B: tRNA pseudouridine synthase B


Theoretical massNumber of molelcules
Total (without water)42,6452
Polymers42,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.975, 134.975, 139.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

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


Mass: 7101.249 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein tRNA pseudouridine synthase B / tRNA pseudouridine 55 synthase / Psi55 synthase / Pseudouridylate synthase / Uracil hydrolyase


Mass: 35544.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: truB / Plasmid: PLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q9WZW0, pseudouridylate synthase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density meas: 65.5 Mg/m3 / Density % sol: 65.5 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 8 / Details: PEG6000, pH 8.0, VAPOR DIFFUSION, temperature 278K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG600011
2H2O11
3PEG600012
4H2O12

-
Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C10.9793
SYNCHROTRONAPS 19-ID20.9797, 0.9800, 0.9574
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97971
30.981
40.95741
ReflectionResolution: 3→50 Å / Num. all: 22770 / Num. obs: 26335 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Rsym value: 0.046 / Net I/σ(I): 15.7

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 3→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.318 1844 Random
Rwork0.261 --
all-22872 -
obs-21028 -
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 938 0 188 5302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0083
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

+
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