EMDB-1063: 80S RNC-SRP complex fron canis sp.

Database / ID

EM DATA BANK (EMDB) / 1063

Sample Name / Map Annotation

80S RNC-SRP complex fron canis sp.
Structure of signal recognition particle interacting with elongation arested ribosome

Authors

Halic M, Becker T, Pool MR, Spahn CM, Grassucci RA, Frank J, Beckmann R

Movies

Movie Page

Related Entries

PDB-1ry1
CiteFit

Cite: data citing same article

Fit: output model of fitting

Last Update

2003-12-19

Map Release Date

2004-12-19

EMDB Sites

EMDB @EBI (EU)

EMDB @RCSB (USA)

Article

Article	Nature, Vol. 427, Issue 6977, Page 808-14, Year 2004
Title	Structure of the signal recognition particle interacting with the elongation-arrested ribosome.
Authors	Mario Halic, Thomas Becker, Martin R Pool, Christian M T Spahn, Robert A Grassucci, Joachim Frank, Roland Beckmann
Affiliation	Institute of Biochemistry, Charité, University Medical School, Humboldt University of Berlin, Monbijoustrasse 2, 10117 Berlin, Germany.
Chemicals	Protein Sorting Signals, Signal Recognition Particle
Keywords	Animals, Base Sequence, Binding Sites, Cryoelectron Microscopy, Mammals, Models, Biological, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Peptide Chain Elongation, Translational, Protein Sorting Signals, Protein Structure, Quaternary, Protein Structure, Tertiary, Ribosomes, Signal Recognition Particle, Structure-Activity Relationship
Links	PubMed: 14985753 DOI: 10.1038/nature02342

Map

File

emd_1063.map ( map file in CCP4 format, 8789 KB )

Projections

Density

Contour Level (movie #1):	0.0007363
Minimum:	-0.00066
Maximum:	0.00216
Average:	0.00003
Standard dev.:	-

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	130	130	130
Origin :	0 A	0 A	0 A
Limit :	129 A	129 A	129 A
Spacing :	130 A	130 A	130 A

Unit Cell

A = 130.000 A , B = 130.000 A , C = 130.000 A ,
alpha = 90.000 degrees , beta = 90.000 degrees , gamma = 90.000 degrees

Pixel Spacing

	X	Y	Z
EMDB info.	3.26	3.26	3.26
CCP4 map header	1	1	1
EM Navigator Movie #1	3.26	3.26	3.26

CCP4 map header info

under construction!

map	MAP
mode	2
A/pix X/Y/Z	1	1	1
M x/y/z	130	130	130
origin x/y/z	0.000	0.000	0.000
length x/y/z	130.000	130.000	130.000
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	0	0	52
NX/NY/NZ	128	128	55
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	130	130	130
start NC,NX/NR,NY/NS,NZ	0	0	0
NC,NX/NR,NY/NS,NZ	130	130	130
D min/max/mean	-0.001	0.002	0.000

Details

CONVERTED FROM SPIDER TO CCP4 USINGSPIDER
Created by IMAGIC: CCP4 image= srp_ccp4_130.rib19-12-20 18:10:08

Annotation Details

Structure of signal recognition particle interacting with elongation arested ribosome

Supplement

Sample

Name	80S RNC-SRP complex fron canis sp.
Aggregation State	single particle
Oligomeric State	one srp binds one ribosome
Number of Components	3
Component #1: ribosome-eukaryote - 80S RNC
Scientific name	80S ribosome
Common Name	80S RNC
Theoretical Mass	4 MDa
Experimental Mass	4 MDa
Details	q
Eukaryote	ALL
Component #2: ligand - SRP
Scientific name	mammalian SRP
Common Name	SRP
Theoretical Mass	0.4 MDa
Experimental Mass	0.4 MDa
Details	q
Oligomeric Details	monomer
Number of Copies	1
Strain	beagle
Mutant	No
Natural Source	Tissue: pancreas Cell: secretory cells Organ: ER Cell Location: ER
Engineered Source	Exp System: dog
Component #3: ligand - tRNA
Scientific name	tRNA
Theoretical Mass	0.025 MDa
Experimental Mass	0.025 MDa
Details	q
Oligomeric Details	monomer
Number of Copies	1
Mutant	No
Engineered Source	Exp System: wheat germ

Experiment

Sample Preparation
Vitrification
Cryogen Name	ETHANE
Imaging
Microscope	FEI TECNAI F30
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	300 kV
Electron Dose	10 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	1000 nM - 4300 nM
Specimen Holder
Holder	Eucentric ( GATAN LIQUID NITROGEN )
Camera
Detector	KODAK SO163
Image Scans
Scanner	OTHER

Processing

3D Reconstruction

Algorithm

projection matching

Software

spider

Resolution By Author

12.0

Resolution Method

FSC at 0.5 cut-off

Atomic Model Fitting

Model #0

PDB Entry ID

PDB-1ry1

Details

The domains were separately fitted by manual docking using program O

Fitted Coordinate

PDB entry ID

PDB-1ry1

Download

Data from EMDB

Header Information

emd-1063.xml ( XML format, 6,202 byte )

Map Data

emd_1063.map.gz ( 8,290,361 byte )Details

Others

1063_corresponding_PDB.map.gz ( 8,292,431 byte )

FTP site (EMDB mirror)

EMD-1063

Data from PDBj EM Navigator

movie #1

	ASF format (for windows) ( 5,712,431 byte ) MOV format (for Mac) ( 5,656,536 byte ) FLV format (for web page) ( 5,747,323 byte ) Session file for UCSF-Chimera ( 20,378 byte )

movie #2

	ASF format (for windows) ( 5,680,431 byte ) MOV format (for Mac) ( 5,627,101 byte ) FLV format (for web page) ( 5,744,069 byte ) Session file for UCSF-Chimera ( 20,933 byte )