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Structure of the signal recognition particle interacting with the elongation-arrested ribosome

by single particle reconstruction, at 12 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1063, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1ry1
TitleStructure of the signal recognition particle interacting with the elongation-arrested ribosome
Descriptorsignal receptor proteins/RNA Complex
KeywordsTRANSLATION, signal recognition particle, RNA binding
AuthorsHalic, M., Becker, T., Pool, M.R., Spahn, C.M., Grassucci, R.A., Frank, J., Beckmann, R.
DateDeposition: 2003-12-19, Release: 2004-04-20
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1063, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1063

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Article
Citation - primary
ArticleNature, Vol. 427, Issue 6977, Page 808-14, Year 2004
TitleStructure of the signal recognition particle interacting with the elongation-arrested ribosome.
AuthorsMario 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.
KeywordsAnimals, 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
LinksPubMed: 14985753, DOI: 10.1038/nature02342
Components
ID 1 : ALU DOMAIN (RNA FRAGMENTS)
Image
DescriptionALU DOMAIN (RNA FRAGMENTS)
Typepolyribonucleotide
Formula weight16277.722 Da
Number of molecules1
ID1
SourceMethod: Obtained synthetically
LinksSequence view
ID 2 : ALU DOMAIN (SRP9, SRP14 + RNA)
Image
DescriptionALU DOMAIN (SRP9, SRP14 + RNA)
Typepolyribonucleotide
Formula weight41566.973 Da
Number of molecules1
ID2
SourceMethod: Obtained synthetically
LinksSequence view
ID 3 : fragment of 7S RNA
Image
Descriptionfragment of 7S RNA
Typepolyribonucleotide
Formula weight8784.338 Da
Number of molecules1
ID3
SourceMethod: Obtained synthetically
LinksSequence view
ID 4 : RNA (31-MER)
Image
DescriptionRNA (31-MER)
Typepolyribonucleotide
Formula weight9807.904 Da
Number of molecules1
ID4
SourceMethod: Obtained synthetically
LinksSequence view
ID 5 : RNA (5'-R(P*GP*UP*UP*CP*UP*GP*GP*GP*CP*UP*GP*UP*AP*GP*UP*GP*CP*GP*CP*UP*AP*UP*GP*C)-3')
Image
DescriptionRNA (5'-R(P*GP*UP*UP*CP*UP*GP*GP*GP*CP*UP*GP*UP*AP*GP*UP*GP*CP*GP*CP*UP*AP*UP*GP*C)-3')
Typepolyribonucleotide
Formula weight7695.595 Da
Number of molecules1
ID5
SourceMethod: Obtained synthetically
LinksSequence view
ID 6 : RNA (5'-R(*CP*AP*AP*UP*AP*GP*CP*CP*AP*CP*UP*GP*CP*AP*CP*UP*CP*CP*AP*G)-3')
Image
DescriptionRNA (5'-R(*CP*AP*AP*UP*AP*GP*CP*CP*AP*CP*UP*GP*CP*AP*CP*UP*CP*CP*AP*G)-3')
Typepolyribonucleotide
Formula weight6325.890 Da
Number of molecules1
ID6
SourceMethod: Obtained synthetically
LinksSequence view
ID 7 : RNA (5'-R(P*CP*GP*AP*UP*CP*GP*GP*GP*UP*GP*UP*C)-3')
Image
DescriptionRNA (5'-R(P*CP*GP*AP*UP*CP*GP*GP*GP*UP*GP*UP*C)-3')
Typepolyribonucleotide
Formula weight3844.346 Da
Number of molecules1
ID7
SourceMethod: Obtained synthetically
LinksSequence view
ID 8 : RNA (5'-R(P*AP*UP*CP*GP*CP*GP*CP*CP*UP*GP*UP*G)-3')
Image
DescriptionRNA (5'-R(P*AP*UP*CP*GP*CP*GP*CP*CP*UP*GP*UP*G)-3')
Typepolyribonucleotide
Formula weight3804.322 Da
Number of molecules1
ID8
SourceMethod: Obtained synthetically
LinksSequence view
ID 9 : SRP9
Image
DescriptionPROTEIN (Signal recognition particle 9 kDa protein)
Typepolypeptide(L)
Formula weight9996.644 Da
Number of molecules1
ID9
SourceMethod: Isolated from a genetically manipulated source
Gene: human, Homo, SRP9, ID:9606, Homo sapiens
LinksUniProt: P49458, Sequence view
ID 10 : SRP14, 18 kDa ALU RNA binding protein
Image
DescriptionPROTEIN (Signal recognition particle 14 kDa protein)
Typepolypeptide(L)
Formula weight12114.332 Da
Number of molecules1
ID10
SourceMethod: Isolated from a genetically manipulated source
Gene: human, Homo, SRP14, ID:9606, Homo sapiens
LinksUniProt: P37108, Sequence view
ID 11 : SRP19
Image
DescriptionPROTEIN (Signal recognition particle 19 kDa protein)
Typepolypeptide(L)
Formula weight12561.778 Da
Number of molecules1
ID11
SourceMethod: Isolated from a genetically manipulated source
Gene: human, Homo, SRP19, ID:9606, Homo sapiens
LinksUniProt: P09132, Sequence view
ID 12 : Fifty-four homolog
Image
DescriptionSignal recognition particle protein
Typepolypeptide(L)
Formula weight32472.762 Da
Number of molecules1
ID12
SourceMethod: Isolated from a genetically manipulated source
Gene: Thermus, FFH, ID:271, Thermus aquaticus
LinksUniProt: O07347, Sequence view
ID 13 : SRP54
Image
DescriptionSignal recognition particle 54 kDa protein
Typepolypeptide(L)
Formula weight12473.510 Da
Number of molecules1
ID13
SourceMethod: Isolated from a genetically manipulated source
Gene: house mouse, Mus, SRP54, ID:10090, Mus musculus
LinksUniProt: P14576, Sequence view
ID 14 : Rhodopsin
Image
DescriptionRhodopsin
Typepolypeptide(L)
Formula weight2121.567 Da
Number of molecules1
ID14
SourceMethod: Isolated from a genetically manipulated source
Gene: bottlenosed dolphin, Tursiops, RHO, ID:9739, Tursiops truncatus
LinksUniProt: O62798, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameCOMPLEX SAMPLE CONCENTRATION (MG ML-1) :
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.4
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsPLUNGED INTO ETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F20
Date2000-01-01
DetailsSAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage160 kV
Electron dose1000 e/A**2
Illumination modeFLOOD BEAM LOW DOSE
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 52000 X, Nominal: 51000 X
CsNominal: 2 mm
Nominal defocusMax: 45000 nm, Min: 10000 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature95 Kelvin
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images75
Processing
2D projection selection
Software nameSPIDER
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
DetailsThe 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 nameSPIDER
Refine
Refine idELECTRON MICROSCOPY
Ls d res high12 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high12
Total atoms11794
Nucleic acid atoms6459
Protein atoms5335
Download
PDB format
Allpdb1ry1.ent.gz
pdb1ry1.ent (uncompressed file)
Header onlypdb1ry1.ent.gz
mmCIF format
mmCIF1ry1.cif.gz
XML format
All1ry1.xml.gz
No-atom1ry1-noatom.xml.gz
Ext-atom1ry1-extatom.xml.gz
Movie files
movie #1
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.webm (WebM/VP8 format), 3.4 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.6 MB