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PSRP1 is not a bona fide ribosomal protein, but a stress response factor

by single particle reconstruction, at 9.8 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 30, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 30, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5125
AuthorsSharma MR, Donhofer A, Barat C, Datta P, Fucini P, Wilson DN, Agrawal RK
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 30, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 30, Made by UCSF CHIMERA

Supplemental images

EMDB figure
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Related Structure Data
Related Entries

EMDB-5126
Cite

Cite: data citing same article

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Diagram

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List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Biol. Chem., Vol. 285, Issue 6, Page 4006-14, Year 2010
TitlePSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G).
AuthorsManjuli R Sharma, Alexandra Dönhöfer, Chandana Barat, Viter Marquez, Partha P Datta, Paola Fucini, Daniel N Wilson, Rajendra K Agrawal
New York State Department of Health, Division of Translational Medicine, Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA.
KeywordsAmino Acid Sequence, Binding Sites (genetics), Carrier Proteins (chemistry), Cryoelectron Microscopy, Crystallography, X-Ray, Electrophoresis, Polyacrylamide Gel, Escherichia coli (metabolism), Models, Molecular, Molecular Sequence Data, Plant Proteins (chemistry), Plastids (metabolism), Protein Binding, Protein Conformation, Protein Structure, Tertiary, Ribosomal Proteins (chemistry), Ribosome Subunits (chemistry), Ribosomes (chemistry), Sequence Homology, Amino Acid, Spinacia oleracea (genetics)
LinksDOI: 10.1074/jbc.M109.062299, PubMed: 19965869, PMC: PMC2823542
Map
FileEMD-5125.map ( map file in CCP4 format, 8790 KB )
Projections & SlicesSize of images:
AxesZ (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:30 (by author), 30 (movie #1):
Minimum - Maximum: -120.19511414 - 276.03640747
Average (Standard dev.): 2.53906465 (27.40571404)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 130 130 130
Origin : 0 0 0
Limit : 129 129 129
Spacing : 130 130 130
Unit CellA = 358.8 A , B = 358.8 A , C = 358.8 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 2.76 A , Y = 2.76 A , Z = 2.76 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.762.762.76
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z358.800358.800358.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-120.195276.0362.539
Annotation Details70S E.coli Ribosome with PSRP1, in vitro
Supplement
Sample
Name70S E.coli ribosome with PSRP1 in vitro
Number of Components2
Theoretical Mass2.8 MDa
Experimental Mass2.8 MDa
Component #1: ribosome-prokaryote - 70S Ribosome
Scientific name70S Ribosome
Theoretical Mass2.5 MDa
Experimental Mass2.5 MDa
Scientific Name of SpeciesEscherichia coli (NCBI Taxonomy: 562)

ProkaryoteLSU 50S, SSU 30S
Recombinant expressionNo
Component #2: ligand - PSRP1
Scientific nameplastid specific ribosomal protein-1
Common NamePSRP1
Theoretical Mass0.27 MDa
Experimental Mass0.27 MDa
Scientific Name of SpeciesSpinacia oleracea (NCBI Taxonomy: 3562)
Common Name of SpeciesSpinach
Recombinant expressionNo
Natural SourceOrganelle: Chloroplast
Experiment
Sample Preparation
Specimen Stateparticle
Specimen Support Details300 mesh coper grid
BufferDetails: 20mM Hepes-KOH, 8.2mM MgCl2, 80mM NH4Cl, 4mM beta-mercaptoethanol
pH: 7.6
Vitrification
MethodBlot for 3 seconds then plunge
Cryogen NameETHANE
DetailsVitrification instrument: Plunger
Humidity80
InstrumentHOMEMADE PLUNGER
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose24 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X, Calibrated: 50760 X
Imaging ModeBRIGHT FIELD
Defocus1200 nm - 4200 nm
Specimen Holder
HolderEucentric ( GATAN LIQUID NITROGEN )
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images53
Sampling Size14 microns
Quant Bit Number12
Processing
Methodsingle particle reconstruction
3 D reconstruction
Algorithmprojection matching
SoftwareSpider
CTF CorrectionEach Micrograph
Resolution By Author9.8
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Class Averages18
Applied SymmetryC1 (asymmetric)
Number of Projections32611
Download
Data from EMDB
Header (meta data in XML format)emd-5125.xml (7.7 KB)
Map dataemd_5125.map.gz (7.8 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5125
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 26.4 KB