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PDBj>EM Navigator>Detail page - EMDB-2053

Electron Microscopy of THO complex

by single particle reconstruction, at 17 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2.52, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 2.52, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2053
AuthorsPena A, Gewartowski K, Mroczek S, Cuellar J, Szykowska A, Prokop A, Czarnocki-Cieciura M, Piwowarski J, Tous C, Aguilera A, Carrascosa JL, Valpuesta JM, Dziembowski A
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2.52, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 2.52, Made by UCSF CHIMERA

Supplemental images

image2053.jpeg
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

PDB-3j2d

EMDB-1877

PDB-3j2c

EMDB-5498
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 31, Issue 6, Page 1605-16, Year 2012
TitleArchitecture and nucleic acids recognition mechanism of the THO complex, an mRNP assembly factor.
AuthorsAlvaro Peña, Kamil Gewartowski, Seweryn Mroczek, Jorge Cuéllar, Aleksandra Szykowska, Andrzej Prokop, Mariusz Czarnocki-Cieciura, Jan Piwowarski, Cristina Tous, Andrés Aguilera, José L Carrascosa, José María Valpuesta, Andrzej Dziembowski
Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
KeywordsAdenosine Triphosphatases (genetics, 3.6.1.-), Binding Sites, Chromatin (genetics), DNA-Binding Proteins (chemistry), HPR1 protein, S cerevisiae, MFT1 protein, S cerevisiae (136253-29-7), Nuclear Proteins (chemistry), Nucleic Acids (metabolism), Protein Binding, RLR1 protein, S cerevisiae, RNA, Messenger (genetics), RNA-Binding Proteins (genetics), RNA-dependent ATPase (3.6.1.-), Ribonucleoproteins (genetics), Saccharomyces cerevisiae (genetics), Saccharomyces cerevisiae Proteins (chemistry), Thp2 protein, S cerevisiae, Transcription Factors (chemistry), Transcription, Genetic (genetics), YRA1 protein, S cerevisiae, messenger ribonucleoprotein
LinksDOI: 10.1038/emboj.2012.10, PubMed: 22314234, PMC: PMC3321177
Map
FileEMD-2053.map ( map file in CCP4 format, 10978 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:2.52 (by author), 2.52 (movie #1):
Minimum - Maximum: -0.57409996 - 12.31480503
Average (Standard dev.): 1.08922005 (0.72266853)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 140 140 140
Origin : -70 -70 -70
Limit : 69 69 69
Spacing : 140 140 140
Unit CellA = 326.19998 A , B = 326.19998 A , C = 326.19998 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 2.33 A , Y = 2.33 A , Z = 2.33 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.332.332.33
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z326.200326.200326.200
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS140140140
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.57412.3151.089
Annotation DetailsReconstruction of yeast THO complex composed of Tho2, Hpr1, Mft1, Thp2, and Tex1 subunits
Supplement
Images
Images

image2053.jpeg
Sample
NameYeast five-subunit THO complex
Number of Components5
Oligomeric StateOne heteropentamer composed of Tho2, Hpr1, Mft1, Thp2 an Tex1 subunits
Theoretical Mass395 MDa
Mass-estimation MethodGel Filtration and Mass Spectrometry
Experimental Mass395 MDa
Component #1: protein - Rlr1
Scientific nameTho2
Common NameRlr1
Theoretical Mass180 MDa
Experimental Mass180 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)

Common Name of SpeciesBaker's Yeast
Recombinant expressionYes
Engineered SourceExp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Component #2: protein - Hpr1
Scientific nameHpr1
Theoretical Mass90 MDa
Experimental Mass90 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of SpeciesBaker's Yeast
Recombinant expressionYes
Engineered SourceExp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Component #3: protein - MFT52
Scientific nameMft1
Common NameMFT52
Theoretical Mass45 MDa
Experimental Mass45 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of SpeciesBaker's Yeast
Recombinant expressionYes
Engineered SourceExp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Component #4: protein - Thp2
Scientific nameThp2
Theoretical Mass30 MDa
Experimental Mass30 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of SpeciesBaker's Yeast
Recombinant expressionYes
Engineered SourceExp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Component #5: protein - Tex1
Scientific nameTex1
Theoretical Mass50 MDa
Experimental Mass50 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of SpeciesBaker's Yeast
Recombinant expressionYes
Engineered SourceExp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Experiment
Sample Preparation
StainingSamples were applied onto carbon-coated copper grids and stained with 2% uranyl acetate for 1 min
Specimen Conc0.35 mg/ml
Specimen Support Details200 mesh carbon-coated copper grids, glow discharged
Specimen Stateparticle
BufferDetails: 10 mM Tris_HCl, 450 mM NaCl
pH: 8.0
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeJEOL 1200EXII
Date15-JUN-2009
Electron Gun
Electron SourceTUNGSTEN HAIRPIN
Accelerating Voltage100 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 60000 X,
AstigmatismObjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs5.6 mm
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 3000 nm
Specimen Holder
Holder ( JEOL )
Tilt Angle0 degrees - 0 degrees
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images250
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmCommon lines, iterative angular refinement , projection matching
Euler Angles DetailsSPIDER protocol
SoftwareEMAN,Spider,XMIPP
CTF CorrectionN. Grigorieffs CTFFIND
Resolution By Author17
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Class Averages15
Number of Projections14115
DetailsIndividual particles were manually selected using XMIPP software package.
Download
Data from EMDB
Header (meta data in XML format)emd-2053.xml (10.7 KB)
Map dataemd_2053.map.gz (8.3 MB)
Imagesimage2053.jpeg (20.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2053
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.8 KB