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Structure of tmRNA-(SmpB)2 complex as inferred from cryo-EM

by single particle reconstruction, at 13.6 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1310, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1310, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2ob7
TitleStructure of tmRNA-(SmpB)2 complex as inferred from cryo-EM
DescriptorSsrA-binding protein/RNA Complex
KeywordsRNA BINDING PROTEIN/RNA, tmRNA, SmpB, RNA BINDING PROTEIN-RNA COMPLEX
AuthorsFrank, J., Felden, B., Gillet, R., Li, W.
DateDeposition: 2006-12-18, Release: 2007-01-23
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1310, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1310, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1310

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Article
Citation - primary
ArticleJ. Biol. Chem., Vol. 282, Issue 9, Page 6356-63, Year 2007
TitleScaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
AuthorsReynald Gillet, Sukhjit Kaur, Wen Li, Marc Hallier, Brice Felden, Joachim Frank
Université de Rennes I, IFR 140, UPRES JE 2311, INSERM U835 Biochimie Pharmaceutique, 2 Avenue du Professeur Léon Bernard, 35043 Rennes, France.
KeywordsCryoelectron Microscopy, Macromolecular Substances (metabolism), Protein Binding, Protein Biosynthesis, RNA, Transfer (metabolism, 9014-25-9), RNA-Binding Proteins (metabolism), Ribosomal Proteins (metabolism), Thermus thermophilus (genetics), ribosomal protein S1, small protein B
LinksDOI: 10.1074/jbc.M609658200, PubMed: 17179154, PMC: PMC3230075
Citation - 1
ArticleProc.Natl.Acad.Sci.USA, Vol. 103, Page: 16484 - 16489, Year: 2006,
TitleCryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome
AuthorsKaur, S., Gillet, R., Li, W., Gursky, R., Frank, J.
Citation - 2
ArticleScience, Vol. 300, Page: 127 - 130, Year: 2003,
TitleVisualizing tmRNA entry into a stalled ribosome
AuthorsValle, M., Gillet, R., Kaur, K., Henne, A., Ramakrishnan, V., Frank, J.
Components
ID 1 : transfer-messenger RNA
Image
Descriptiontransfer-messenger RNA
Typepolyribonucleotide
Formula weight105729.453 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksSequence view
ID 2 : 16S ribosomal RNA
Image
Description16S ribosomal RNA
Typepolyribonucleotide
Formula weight27987.885 Da
Number of molecules1
ID2
Detailshelix 44 of 30S ribosomal subunit
SourceMethod: Isolated from a natural source
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksSequence view
ID 3 : SsrA-binding protein
Image
DescriptionSsrA-binding protein
Typepolypeptide(L)
Formula weight18440.992 Da
Number of molecules2
ID3
SourceMethod: Isolated from a natural source
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksSequence view
Sample
Assembly
Aggregation statePARTICLE
Detailssee Experimental Procedures in Kaur et al. (PNAS). [Deposition refers to structure of tmRNA-(SmpB)2 complex derived by fitting of EM map from Kaur et al. Fitting was modified in Gillet et al.]
NameBinding of transfer messenger RNA with two SmpBs
Entity assembly
Assembly-ID1
NamePre-accommodated ribosomal trans-translation complex: T. thermophilus 70S-mRNA-(P-site tRNA)-tmRNA-(SmpB)2-(EF-Tu)-GDP-kirromycin
Buffer
Namepolimix
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample concentration32 mg/ml
Sample support
DetailsThis grid plus sample was kept at -80 degree C for several days before use.
Vitrification
DetailsBlot for 5 seconds before plunging. Rapid plunge freezing in liquid ethane.
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: F20
Date2004-06-01
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage200 kV
Electron dose1500 e/A**2
Illumination modeFLOOD BEAM LOW DOSE
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 49000 X, Nominal: 55000 X
CsNominal: 2 mm
Nominal defocusMax: 3635 nm, Min: 1475 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature296 Kelvin
Detector
TypeKODAK SO163 FILM
Processing
2D projection selection
Software nameO
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
CTF correction methodCTF correction of each defocus group reconstruction, by Wiener filtering
Methodsingle particle reconstruction
Nominal pixel size2.82 A/pix
Resolution13.6 A
3D fitting
Methodmanual fitting using stereo visualization
Refinement ProtocolManual
Refinement SpaceREAL
Software nameO
3D fitting list
3D Fitting ID1
PDB entry ID1P6V for SmpB and TLD of tmRNA
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms651
Nucleic acid atoms414
Protein atoms237
Download
PDB format
Allpdb2ob7.ent.gz
pdb2ob7.ent (uncompressed file)
Header onlypdb2ob7.ent.gz
mmCIF format
mmCIF2ob7.cif.gz
XML format
All2ob7.xml.gz
No-atom2ob7-noatom.xml.gz
Ext-atom2ob7-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.3 MB
.webm (WebM/VP8 format), 3.3 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.6 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.9 MB