EMDB-1283: Molecular architecture and conformational flexibility ...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1283
Authors	Kostek SA, Grob P, De Carlo S, Lipscomb JS, Garczarek F, Nogales E
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.32, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.32, Made by UCSF CHIMERA
Supplemental images	1283.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1282 Cite EMDB-1284 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-1711 EMDB-1284 PDB-1suv EMDB-1242 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Structure, Vol. 14, Issue 11, Page 1691-700, Year 2006
Title	Molecular architecture and conformational flexibility of human RNA polymerase II.
Authors	Seth 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.
Keywords	Cryoelectron 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
Links	PII: S0969-2126(06)00397-2, DOI: 10.1016/j.str.2006.09.011, PubMed: 17098194

Map

File

EMD-1283.map ( map file in CCP4 format, 6913 KB )

Projections & Slices

Size of images:

Axes	Z (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:	0.126, 0.32 (movie #1):
Minimum - Maximum:	-0.158582 - 0.587113
Average (Standard dev.):	0.0115372 (0.0722153)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	120	120	120
Origin :	-60	-60	-60
Limit :	59	59	59
Spacing :	120	120	120

Unit Cell

A = 300 A , B = 300 A , C = 300 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 2.5 A , Y = 2.5 A , Z = 2.5 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	2.5	2.5	2.5
M x/y/z	120	120	120
origin x/y/z	0.000	0.000	0.000
length x/y/z	300.000	300.000	300.000
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-184	-184	-183
NX/NY/NZ	368	368	368
MAP C/R/S	1	2	3
start NC/NR/NS	-60	-60	-60
NC/NR/NS	120	120	120
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-0.159	0.587	0.012

Annotation Details

Conformation 1

Supplement
Images
Images	1283.gif

Sample
Name	human RNA Polymerase II
Oligomeric State	12 subunit complex
Number of Components	12
Experimental Mass	0.5 MDa
Theoretical Mass	0.52 MDa
Component #1: protein - Rpb1
Scientific name	Rpb1
Experimental Mass	0.22 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Organelle: Nucleus Cell: HeLa
Component #2: protein - Rpb2
Scientific name	Rpb2
Experimental Mass	0.13 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Cell: HeLa Organelle: Nucleus
Component #3: protein - Rpb3
Scientific name	Rpb3
Experimental Mass	0.03 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Organelle: Nucleus Cell: HeLa
Component #4: protein - Rpb4
Scientific name	Rpb4
Experimental Mass	0.02 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Organelle: Nucleus Cell: HeLa
Component #5: protein - Rpb5
Scientific name	Rpb5
Experimental Mass	0.02 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Organelle: Nucleus Cell: HeLa
Component #6: protein - Rpb6
Scientific name	Rpb6
Experimental Mass	0.01 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Organelle: Nucleus Cell: HeLa
Component #7: protein - Rpb7
Scientific name	Rpb7
Experimental Mass	0.02 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Organelle: Nucleus Cell: HeLa
Component #8: protein - Rpb8
Scientific name	Rpb8
Experimental Mass	0.02 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Cell: HeLa Organelle: Nucleus
Component #9: protein - Rpb9
Scientific name	Rpb9
Experimental Mass	0.01 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Cell: HeLa Organelle: Nucleus
Component #10: protein - Rpb10
Scientific name	Rpb10
Experimental Mass	0.01 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Cell: HeLa Organelle: Nucleus
Component #11: protein - Rpb11
Scientific name	Rpb11
Experimental Mass	0.01 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Cell: HeLa Organelle: Nucleus
Component #12: protein - Rpb12
Scientific name	Rpb12
Experimental Mass	0.01 MDa
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	No
Natural Source	Cell: HeLa Organelle: Nucleus

Experiment
Sample Preparation
Specimen Conc	0.01 mg/ml
Staining	cryo-negative staining in a saturated solution of ammonium molybdate neutralized to a pH of 7.2. with 10 N NaOH
Specimen Support Details	400 mesh copper grid
Specimen State	particle
Buffer	Details: 200mM (NH4)2SO4, 25mM Hepes, 0.2M EDTA, 0.05% NP-40 pH: 7.9
Vitrification
Cryogen Name	ETHANE
Temperature	90 Kelvin
Method	stained with ammonium molybdate before plunging
Imaging
Microscope	FEI/PHILIPS CM200FEG
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	17 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X, Calibrated: 50280 X
Nominal Cs	2.2 mm
Imaging Mode	BRIGHT FIELD
Defocus	1200 nm - 3600 nm
Specimen Holder
Holder	side entry ( GATAN LIQUID NITROGEN )
Temperature	90 Kelvin
Camera
Detector	Kodak SO163 film
Image Acquisition
Number of Digital Images	19
Sampling Size	6.3 microns
Od Range	1.0
Quant Bit Number	14
Scanner	OTHER

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Fourier method
Software	FREALIGN
CTF Correction	each micrograph
Resolution By Author	20
Resolution Method	FSC at 0.143 cut-off
Single Particle
Number of Projections	3406

Download

Data from EMDB

Header (meta data in XML format)

emd-1283.xml (15 KB)

Map data

emd_1283.map.gz (5.7 MB)

Images

1283.gif (21.4 KB)

FTP directory

ftp://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