PDB-1ry1: Structure of the signal recognition particle interactin...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 1ry1
Title	Structure of the signal recognition particle interacting with the elongation-arrested ribosome
Descriptor	signal receptor proteins/RNA Complex
Keywords	TRANSLATION, signal recognition particle, RNA binding
Authors	Halic, M., Becker, T., Pool, M.R., Spahn, C.M., Grassucci, R.A., Frank, J., Beckmann, R.
Date	Deposition: 2003-12-19, Release: 2004-04-20
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-1063, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1063 CiteFit PDB-2xkv Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-2280 EMDB-1972 List of similar structure data about Omokage system

Article
Citation - primary
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 Institute of Biochemistry, Charité, University Medical School, Humboldt University of Berlin, Monbijoustrasse 2, 10117 Berlin, Germany.
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 (genetics), Protein Structure, Quaternary, Protein Structure, Tertiary, Ribosomes (chemistry), Signal Recognition Particle (chemistry), Structure-Activity Relationship
Links	PubMed: 14985753, DOI: 10.1038/nature02342

Components
ID 1 : ALU DOMAIN (RNA FRAGMENTS)
Image
Description	ALU DOMAIN (RNA FRAGMENTS)
Type	polymer
Formula weight	16277.722 Da
Number of molecules	1
Source	Method: Obtained synthetically
Links	Sequence view
ID 2 : ALU DOMAIN (SRP9, SRP14 + RNA)
Image
Description	ALU DOMAIN (SRP9, SRP14 + RNA)
Type	polymer
Formula weight	41566.973 Da
Number of molecules	1
Source	Method: Obtained synthetically
Links	Sequence view
ID 3 : fragment of 7S RNA
Image
Description	fragment of 7S RNA
Type	polymer
Formula weight	8784.338 Da
Number of molecules	1
Source	Method: Obtained synthetically
Links	Sequence view
ID 4 : RNA (31-MER)
Image
Description	RNA (31-MER)
Type	polymer
Formula weight	9807.904 Da
Number of molecules	1
Source	Method: Obtained synthetically
Links	Sequence view
ID 5 : RNA (5'-R(PGPUPUPCPUPGPGPGPCPUPGPUPAPGPUPGPCPGPCPUPAPUPGPC)-3')
Image
Description	RNA (5'-R(PGPUPUPCPUPGPGPGPCPUPGPUPAPGPUPGPCPGPCPUPAPUPGPC)-3')
Type	polymer
Formula weight	7695.595 Da
Number of molecules	1
Source	Method: Obtained synthetically
Links	Sequence view
ID 6 : RNA (5'-R(CPAPAPUPAPGPCPCPAPCPUPGPCPAPCPUPCPCPAPG)-3')
Image
Description	RNA (5'-R(CPAPAPUPAPGPCPCPAPCPUPGPCPAPCPUPCPCPAPG)-3')
Type	polymer
Formula weight	6325.890 Da
Number of molecules	1
Source	Method: Obtained synthetically
Links	Sequence view
ID 7 : RNA (5'-R(PCPGPAPUPCPGPGPGPUPGPUPC)-3')
Image
Description	RNA (5'-R(PCPGPAPUPCPGPGPGPUPGPUPC)-3')
Type	polymer
Formula weight	3844.346 Da
Number of molecules	1
Source	Method: Obtained synthetically
Links	Sequence view
ID 8 : RNA (5'-R(PAPUPCPGPCPGPCPCPUPGPUPG)-3')
Image
Description	RNA (5'-R(PAPUPCPGPCPGPCPCPUPGPUPG)-3')
Type	polymer
Formula weight	3804.322 Da
Number of molecules	1
Source	Method: Obtained synthetically
Links	Sequence view
ID 9 : SRP9
Image
Description	PROTEIN (Signal recognition particle 9 kDa protein)
Type	polymer
Formula weight	9996.644 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: human, Homo, SRP9, ID:9606, Homo sapiens
Links	UniProt: P49458, Sequence view
ID 10 : SRP14, 18 kDa ALU RNA binding protein
Image
Description	PROTEIN (Signal recognition particle 14 kDa protein)
Type	polymer
Formula weight	12114.332 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: human, Homo, SRP14, ID:9606, Homo sapiens
Links	UniProt: P37108, Sequence view
ID 11 : SRP19
Image
Description	PROTEIN (Signal recognition particle 19 kDa protein)
Type	polymer
Formula weight	12561.778 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: human, Homo, SRP19, ID:9606, Homo sapiens
Links	UniProt: P09132, Sequence view
ID 12 : Fifty-four homolog
Image
Description	Signal recognition particle protein
Type	polymer
Formula weight	32472.762 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: Thermus, FFH, ID:271, Thermus aquaticus
Links	UniProt: O07347, Sequence view
ID 13 : SRP54
Image
Description	Signal recognition particle 54 kDa protein
Type	polymer
Formula weight	12473.510 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: house mouse, Mus, SRP54, ID:10090, Mus musculus
Links	UniProt: P14576, Sequence view
ID 14 : Rhodopsin
Image
Description	Rhodopsin
Type	polymer
Formula weight	2121.567 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: bottlenosed dolphin, Tursiops, RHO, ID:9739, Tursiops truncatus
Links	UniProt: O62798, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	COMPLEX SAMPLE CONCENTRATION (MG ML-1) :
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.4
Sample support
Details	HOLEY CARBON
Vitrification
Details	PLUNGED INTO ETHANE

Electron Microscopy
Imaging
Microscope	model: FEI TECNAI F20
Date	2000-01-01
Details	SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	160 kV
Electron dose	1000 e/A**2
Illumination mode	FLOOD BEAM LOW DOSE
Lens
Mode	BRIGHT FIELD
Magnification	calibrated: 52000 X, nominal: 51000 X
Cs	nominal: 2 mm
Nominal defocus	max: 45000 nm, min: 10000 nm
Specimen holder
Tilt angle	min: 0 degrees, max: 0 degrees
Temperature	95 Kelvin
Detector
Type	KODAK SO163 FILM
Image scans
Number digital images	75

Processing
2D projection selection
Software name	SPIDER
Single particle entity
Symmetry type	ASYMMETRIC
3D reconstruction
Details	The chains M, N, O, P, Q and R are fragments of a double helical strand of RNA. The author maintains that some of the residues could not be modeled correctly due to limited resolution in this region.
3D fitting
Software name	SPIDER
Refine
Ls d res high	12 A
ID	1
Refine hist
D res high	12
Total atoms	11794
Nucleic acid atoms	6459
Protein atoms	5335