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Coordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray structure aligned to the 70S Cryo-EM map of E.coli ribosome

by single particle reconstruction, at 10.8 A resolution

Movie

Orientation:

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1055, Image by Jmol

#3: Superimposing with simplified surface model of EM map, EMDB-1362, Image by Jmol

#4: Superimposing with simplified surface model of EM map, EMDB-1363, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-1365, Image by Jmol

#6: Superimposing with simplified surface model of EM map, EMDB-1366, Image by Jmol

#7: With PDB-1pn6, PDB-1pn8, Image by Jmol

#8: Superimposing with EM 3D map: EMDB-1055 (with PDB-1pn6, PDB-1pn8), Image by UCSF CHIMERA

#9: Superimposing with EM 3D map: EMDB-1363 (with PDB-1pn6, PDB-1pn8), Image by UCSF CHIMERA

#10: Superimposing with EM 3D map: EMDB-1365 (with PDB-1pn6, PDB-1pn8), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1pn7
TitleCoordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray structure aligned to the 70S Cryo-EM map of E.coli ribosome
DescriptorRNA BINDING PROTEIN/RNA Complex
KeywordsRNA binding protein/RNA, ribosomal protein, tRNA binding protein, tRNA, RNA binding protein-RNA COMPLEX
AuthorsValle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M., Frank, J.
DateDeposition: 2003-06-12, Release: 2003-07-15
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-1055, Image by Jmol

#3: Superimposing with simplified surface model of EM map, EMDB-1362, Image by Jmol

#4: Superimposing with simplified surface model of EM map, EMDB-1363, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-1365, Image by Jmol

#6: Superimposing with simplified surface model of EM map, EMDB-1366, Image by Jmol

#7: With PDB-1pn6, PDB-1pn8, Image by Jmol

#8: Superimposing with EM 3D map: EMDB-1055 (with PDB-1pn6, PDB-1pn8), Image by UCSF CHIMERA

#9: Superimposing with EM 3D map: EMDB-1363 (with PDB-1pn6, PDB-1pn8), Image by UCSF CHIMERA

#10: Superimposing with EM 3D map: EMDB-1365 (with PDB-1pn6, PDB-1pn8), Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1362

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Cite: data citing same article

Fit: target map of fitting

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Article
Citation - primary
ArticleCell, Vol. 114, Issue 1, Page 123-34, Year 2003
TitleLocking and unlocking of ribosomal motions.
AuthorsMikel Valle, Andrey Zavialov, Jayati Sengupta, Urmila Rawat, Måns Ehrenberg, Joachim Frank
Howard Hughes Medical Institute, and Health Research Incororated at the Wadswoth Center, State University of New York, Albany, 12201, USA.
KeywordsBinding Sites (genetics), Cryoelectron Microscopy, Eukaryotic Cells (metabolism), Models, Molecular, Molecular Conformation, Peptide Elongation Factor G (genetics), Peptides (genetics), Protein Biosynthesis (genetics), Protein Structure, Tertiary (genetics), Protein Subunits (genetics), RNA, Messenger (genetics), RNA, Transfer (genetics, 9014-25-9), Ribosomes (genetics), Rotation
LinksPubMed: 12859903, PII: S0092867403004768
Components
ID 1 : P-tRNA
Image
DescriptionP-tRNA
Typepolyribonucleotide
Formula weight20017.092 Da
Number of molecules1
ID1
SourceMethod: Obtained synthetically
LinksSequence view
ID 2 : 30S ribosomal protein S12
Image
Description30S ribosomal protein S12
Typepolypeptide(L)
Formula weight13804.441 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksUniProt: Q5SHN3, Sequence view
ID 3 : 50S ribosomal protein L11
Image
Description50S ribosomal protein L11
Typepolypeptide(L)
Formula weight14295.032 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Genus: Thermotoga
NCBI taxonomy: ID:2336
Organism scientific: Thermotoga maritima
LinksUniProt: P29395, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Entity assembly
Assembly-ID1
NameP-tRNA
Entity assembly
Assembly-ID1
GO-IDGO:0006412
InterPro-IDIPR:006032
Name30S ribosomal protein S12
Entity assembly
Assembly-ID1
GO-IDGO:0006412
InterPro-IDIPR:000911
Name50S ribosomal protein L11
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample concentration32 mg/ml
Sample support
DetailsQuantifoil holley-carbon film grids
Vitrification
DetailsRapid-freezing in liquid ethane
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F20
Date2001-06-01
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage200 kV
Electron dose2000 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 49696 X, Nominal: 50000 X
CsNominal: 2.0 mm
Nominal defocusMax: 4000. nm, Min: 1500. nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature93 Kelvin
Detector
TypeKODAK SO163 FILM
Processing
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
Actual pixel size2.82 A/pix
CTF correction methodCTF correction of 3D-maps by Wiener filtration
DetailsSPIDER package. Crystal Structure of Thermus Thermophilus 70S ribosome
Magnification calibrationTMV
Method3D projection matching; conjugate gradients with regularization
Resolution10.8 A
3D fitting
MethodManual fitting in O
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID1GIX, 1GIY
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms319
Nucleic acid atoms62
Protein atoms257
Download
PDB format
Allpdb1pn7.ent.gz
pdb1pn7.ent (uncompressed file)
Header onlypdb1pn7.ent.gz
mmCIF format
mmCIF1pn7.cif.gz
XML format
All1pn7.xml.gz
No-atom1pn7-noatom.xml.gz
Ext-atom1pn7-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.5 MB
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movie #2
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movie #7
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movie #8
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movie #9
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movie #10
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