[English] 日本語
Yorodumi
- PDB-2gje: Structure of a guideRNA-binding protein complex bound to a gRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gje
TitleStructure of a guideRNA-binding protein complex bound to a gRNA
Components
  • RNA tetramer
  • guide RNA 40-mer
  • mitochondrial RNA-binding protein 1
  • mitochondrial RNA-binding protein 2
KeywordsTRANSLATION/RNA / guide RNA / kRNA editing / RNA binding protein / TRANSLATION-RNA COMPLEX
Function / homology
Function and homology information


RNA modification / mRNA modification / kinetoplast / nuclear lumen / post-transcriptional regulation of gene expression / mRNA binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / RNA binding
Similarity search - Function
Transcriptional Co-activator pc4; Chain A - #40 / SUN domain-containing protein 1, N-terminal / Mitochondrial RNA binding protein MRP / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / GBP21 / Guide RNA binding protein gBP25
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.37 Å
AuthorsSchumacher, M.A. / Karamooz, E. / Zikova, A. / Trantirek, L. / Lukes, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Crystal Structures of T. brucei MRP1/MRP2 Guide-RNA Binding Complex Reveal RNA Matchmaking Mechanism.
Authors: Schumacher, M.A. / Karamooz, E. / Zikova, A. / Trantirek, L. / Lukes, J.
History
DepositionMar 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: guide RNA 40-mer
S: RNA tetramer
A: mitochondrial RNA-binding protein 2
D: mitochondrial RNA-binding protein 1


Theoretical massNumber of molelcules
Total (without water)57,5104
Polymers57,5104
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.600, 157.600, 81.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsMRP1/MRP2 form a heterotetramer with pseudo C4 symmetry ++ RNA single strand

-
Components

#1: RNA chain guide RNA 40-mer


Mass: 12534.474 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA tetramer


Mass: 1586.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein mitochondrial RNA-binding protein 2 / MRP2 / guide RNA-binding protein


Mass: 22055.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: TREU927 / Gene: mrp1 / Plasmid: petduet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q952G2
#4: Protein mitochondrial RNA-binding protein 1 / MRP1


Mass: 21333.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: TREU927 / Gene: mrp2 / Plasmid: petduet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P90629
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: peg 4000, hepes, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Components of the solutions
IDNameCrystal-IDSol-ID
1peg 400011
2hepes11
3isopropanol11
4peg 400012
5hepes12
6isopropanol12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.989 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 3.37→81.6 Å / Num. all: 8830 / Num. obs: 8126 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.37→3.45 Å / % possible all: 70

-
Processing

Software
NameVersionClassification
ADSCdata collection
SCALAdata scaling
EPMRphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.37→69.85 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 6089525.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 606 7.5 %RANDOM
Rwork0.282 ---
all0.2821 8126 --
obs0.2821 8111 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.7629 Å2 / ksol: 0.274147 e/Å3
Displacement parametersBiso mean: 82.1 Å2
Baniso -1Baniso -2Baniso -3
1-11.71 Å23.64 Å20 Å2
2--11.71 Å20 Å2
3----23.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3.37→69.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 377 0 1 2769
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d2.48
LS refinement shellResolution: 3.37→3.58 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 58 6 %
Rwork0.324 913 -
obs--67.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION4ion.top

+
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