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Molecular architecture and conformational flexibility of human RNA polymerase II.

by single particle reconstruction, at 20 A resolution

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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

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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
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)
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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