3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-1283

Molecular architecture and conformational flexibility of human RNA polymerase II.

by single particle reconstruction, at 20 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.32, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.32, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1283
TitleMolecular architecture and conformational flexibility of human RNA polymerase II.
MapConformation 1
Samplehuman RNA Polymerase II
AuthorsKostek SA, Grob P, De Carlo S, Lipscomb JS, Garczarek F, Nogales E
DateDeposition: 2006-10-28, Header release: 2006-10-28, Map release: 2006-10-28, Last update: 2011-05-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.32, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.32, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres
List of similar structure data Omokage searchabout Omokage system
Article
Citation - Primary
ArticleStructure, Vol. 14, Issue 11, Page 1691-700, Year 2006
TitleMolecular architecture and conformational flexibility of human RNA polymerase II.
AuthorsSeth A Kostek, Patricia Grob, Sacha De Carlo, J Slaton Lipscomb, Florian Garczarek, Eva Nogales
Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, California 94720, USA.
KeywordsCryoelectron Microscopy, Fungal Proteins (chemistry), HeLa Cells, Humans, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Microscopy, Electron, Models, Molecular, Molecular Conformation, Protein Conformation, RNA Polymerase II (chemistry, 2.7.7.-), Transcription, Genetic
LinksPII: S0969-2126(06)00397-2, DOI: 10.1016/j.str.2006.09.011, PubMed: 17098194
Map
Fileemd_1283.map.gz ( map file in CCP4 format, 6751 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
120 pix
2.5 A/pix
= 300. A
120 pix
2.5 A/pix
= 300. A
120 pix
2.5 A/pix
= 300. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.126, 0.32 (movie #1):
Minimum - Maximum: -0.158582 - 0.587113
Average (Standard dev.): 0.0115372 (0.0722153)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions120120120
Origin-60-60-60
Limit595959
Spacing120120120
Unit CellA= B= C: 300 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.5 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.52.52.5
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000300.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.1590.5870.012
Annotation DetailsConformation 1
Supplement
Images
Images
Sample
Namehuman RNA Polymerase II
Oligomeric State12 subunit complex
Number of Components12
Experimental Mass0.5MDa
Theoretical Mass0.52MDa
Component #1: protein - Rpb1
Scientific nameRpb1
Experimental Mass0.22 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceOrganelle: Nucleus
Cell: HeLa
Component #2: protein - Rpb2
Scientific nameRpb2
Experimental Mass0.13 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceCell: HeLa
Organelle: Nucleus
Component #3: protein - Rpb3
Scientific nameRpb3
Experimental Mass0.03 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceOrganelle: Nucleus
Cell: HeLa
Component #4: protein - Rpb4
Scientific nameRpb4
Experimental Mass0.02 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceOrganelle: Nucleus
Cell: HeLa
Component #5: protein - Rpb5
Scientific nameRpb5
Experimental Mass0.02 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceOrganelle: Nucleus
Cell: HeLa
Component #6: protein - Rpb6
Scientific nameRpb6
Experimental Mass0.01 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceOrganelle: Nucleus
Cell: HeLa
Component #7: protein - Rpb7
Scientific nameRpb7
Experimental Mass0.02 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceOrganelle: Nucleus
Cell: HeLa
Component #8: protein - Rpb8
Scientific nameRpb8
Experimental Mass0.02 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceCell: HeLa
Organelle: Nucleus
Component #9: protein - Rpb9
Scientific nameRpb9
Experimental Mass0.01 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceCell: HeLa
Organelle: Nucleus
Component #10: protein - Rpb10
Scientific nameRpb10
Experimental Mass0.01 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceCell: HeLa
Organelle: Nucleus
Component #11: protein - Rpb11
Scientific nameRpb11
Experimental Mass0.01 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceCell: HeLa
Organelle: Nucleus
Component #12: protein - Rpb12
Scientific nameRpb12
Experimental Mass0.01 MDa
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceCell: HeLa
Organelle: Nucleus
Experiment
Sample Preparation
Specimen Conc0.01 mg/ml
Stainingcryo-negative staining in a saturated solution of ammonium molybdate neutralized to a pH of 7.2. with 10 N NaOH
Specimen Support Details400 mesh copper grid
Specimen Stateparticle
BufferDetails: 200mM (NH4)2SO4, 25mM Hepes, 0.2M EDTA, 0.05% NP-40
pH: 7.9
Vitrification
Cryogen NameETHANE
Temperature90 Kelvin
Methodstained with ammonium molybdate before plunging
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose17 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 50280
Nominal Cs2.2 mm
Imaging ModeBRIGHT FIELD
Defocus1200 nm - 3600 nm
Specimen Holder
Holderside entry
ModelGATAN LIQUID NITROGEN
Temperature90 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
Number of Digital Images19
Sampling Size6.3
Od Range1
Quant Bit Number14
ScannerOTHER
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmFourier method
SoftwareFREALIGN
CTF Correctioneach micrograph
Resolution By Author20 A
Resolution MethodFSC 0.143
Single Particle
Number of Projections3406
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1283.xml (15.1 KB)
Map dataemd_1283.map.gz (5.7 MB)
Images1283.gif (21.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1283
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 26.8 KB