3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - PDB-3bbn

Homology model for the Spinach chloroplast 30S subunit fitted to 9.4A cryo-EM map of the 70S chlororibosome.

by single particle reconstruction, at 9.4 A resolution

Movie

Orientation:

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1417, Image by Jmol

#3: With PDB-3bbo, PDB-4v61, Image by Jmol

#4: With PDB-, Image by Jmol

#5: Superimposing with EM 3D map: EMDB-1417 (with PDB-3bbo), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3bbn
TitleHomology model for the Spinach chloroplast 30S subunit fitted to 9.4A cryo-EM map of the 70S chlororibosome.
Descriptorsmall ribosomal subunit 30S
KeywordsRIBOSOME, SMALL RIBOSOMAL SUBUNIT, SPINACH CHLOROPLAST RIBOSOME, RIBONUCLEOPROTEIN PARTICLE, MACROMOLECULAR COMPLEX
AuthorsSharma, M.R., Wilson, D.N., Datta, P.P., Barat, C., Schluenzen, F., Fucini, P., Agrawal, R.K.
DateDeposition: 2007-11-09, Release: 2008-05-13
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 simplified surface model of EM map, EMDB-1417, Image by Jmol

#3: With PDB-3bbo, PDB-4v61, Image by Jmol

#4: With PDB-, Image by Jmol

#5: Superimposing with EM 3D map: EMDB-1417 (with PDB-3bbo), Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-1417

CiteFit

PDB-3bbo

CiteSplit

PDB-4v61

CiteSplit

Cite: data citing same article

Fit: target map of fitting

Split: split data constructing the same model

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 104, Issue 49, Page 19315-20, Year 2007
TitleCryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
AuthorsManjuli R Sharma, Daniel N Wilson, Partha P Datta, Chandana Barat, Frank Schluenzen, Paola Fucini, Rajendra K Agrawal
Laboratory of Structural Pathology, Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA.
KeywordsChloroplasts (chemistry), Cryoelectron Microscopy, Crystallography, X-Ray, Evolution, Molecular, Plant Proteins (chemistry), Plastids (chemistry), Protein Conformation, Ribosomal Proteins (chemistry), Ribosome Subunits, Large, Eukaryotic (chemistry), Ribosome Subunits, Small, Eukaryotic (chemistry), Spinacia oleracea (metabolism)
LinksDOI: 10.1073/pnas.0709856104, PubMed: 18042701, PMC: PMC2148287
Components
ID 1 : 16S rRNA
Image
Description16S rRNA
Typepolyribonucleotide
Formula weight483491.750 Da
Number of molecules1
ID1
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksGenBank: 7636084, Sequence view
ID 2 : Ribosomal Protein S2
Image
DescriptionRibosomal Protein S2
Typepolypeptide(L)
Formula weight26092.477 Da
Number of molecules1
ID2
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P08242, Sequence view
ID 3 : Ribosomal Protein S3
Image
DescriptionRibosomal Protein S3
Typepolypeptide(L)
Formula weight24965.348 Da
Number of molecules1
ID3
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P09595, Sequence view
ID 4 : Ribosomal Protein S4
Image
DescriptionRibosomal Protein S4
Typepolypeptide(L)
Formula weight23454.705 Da
Number of molecules1
ID4
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P13788, Sequence view
ID 5 : Ribosomal Protein S5
Image
DescriptionRibosomal Protein S5
Typepolypeptide(L)
Formula weight33626.633 Da
Number of molecules1
ID5
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: Q9ST69, Sequence view
ID 6 : Ribosomal Protein S6
Image
DescriptionRibosomal Protein S6
Typepolypeptide(L)
Formula weight18870.516 Da
Number of molecules1
ID6
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P82403, Sequence view
ID 7 : Ribosomal Protein S7
Image
DescriptionRibosomal Protein S7
Typepolypeptide(L)
Formula weight17378.459 Da
Number of molecules1
ID7
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P82129, Sequence view
ID 8 : Ribosomal Protein S8
Image
DescriptionRibosomal Protein S8
Typepolypeptide(L)
Formula weight15527.367 Da
Number of molecules1
ID8
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P09597, Sequence view
ID 9 : Ribosomal Protein S9
Image
DescriptionRibosomal Protein S9
Typepolypeptide(L)
Formula weight21351.033 Da
Number of molecules1
ID9
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P82278, Sequence view
ID 10 : Ribosomal Protein S10
Image
DescriptionRibosomal Protein S10
Typepolypeptide(L)
Formula weight21632.775 Da
Number of molecules1
ID10
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 11 : Ribosomal Protein S11
Image
DescriptionRibosomal Protein S11
Typepolypeptide(L)
Formula weight15085.819 Da
Number of molecules1
ID11
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P06506, Sequence view
ID 12 : Ribosomal Protein S12
Image
DescriptionRibosomal Protein S12
Typepolypeptide(L)
Formula weight13794.378 Da
Number of molecules1
ID12
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P62128, Sequence view
ID 13 : Ribosomal Protein S13
Image
DescriptionRibosomal Protein S13
Typepolypeptide(L)
Formula weight16306.214 Da
Number of molecules1
ID13
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P82163, Sequence view
ID 14 : Ribosomal Protein S14
Image
DescriptionRibosomal Protein S14
Typepolypeptide(L)
Formula weight11809.930 Da
Number of molecules1
ID14
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P06507, Sequence view
ID 15 : Ribosomal Protein S15
Image
DescriptionRibosomal Protein S15
Typepolypeptide(L)
Formula weight10778.859 Da
Number of molecules1
ID15
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: Q9M3I4, Sequence view
ID 16 : Ribosomal Protein S16
Image
DescriptionRibosomal Protein S16
Typepolypeptide(L)
Formula weight10454.338 Da
Number of molecules1
ID16
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P28807, Sequence view
ID 17 : Ribosomal Protein S17
Image
DescriptionRibosomal Protein S17
Typepolypeptide(L)
Formula weight15828.815 Da
Number of molecules1
ID17
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 18 : Ribosomal Protein S18
Image
DescriptionRibosomal Protein S18
Typepolypeptide(L)
Formula weight12337.539 Da
Number of molecules1
ID18
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: Q9M3K7, Sequence view
ID 19 : Ribosomal Protein S19
Image
DescriptionRibosomal Protein S19
Typepolypeptide(L)
Formula weight10632.598 Da
Number of molecules1
ID19
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P06508, Sequence view
ID 20 : Ribosomal Protein S20
Image
DescriptionRibosomal Protein S20
Typepolypeptide(L)
Formula weight21866.514 Da
Number of molecules1
ID20
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 21 : Ribosomal Protein S21
Image
DescriptionRibosomal Protein S21
Typepolypeptide(L)
Formula weight21701.436 Da
Number of molecules1
ID21
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
Sample
Assembly
Aggregation statePARTICLE
Detailstight couple chloroplast 70S ribosomes
Namespinach 70S chloro-ribosome
Buffer
Name10mM Tris-HCL pH 7.6, 50mM KCL, 10mM MgOAc, 7mM 2-ME
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.6
Vitrification
Details5 microliters applied to the grid then blotted for 3 seconds with Whatman number 1 filter paper before plunging in liquid ethane.
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: Phillips Tecnai F20 FEG
Electron gun
Electron sourceFEG
Accelerating voltage200 kV
Electron dose2000 e/A**2
Illumination modeFlood Beam
Lens
ModeBright Field
MagnificationCalibrated: 50760 X, Nominal: 50000 X
CsNominal: 2 mm
Nominal defocusMax: 3500 nm, Min: 700 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature93 Kelvin
Detector
TypeKodak S0163 Film
Processing
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
Actual pixel size2.76 A/pix
CTF correction methodCTF correction for each Micrograph
DetailsAn 11.5 A E.coli 70S ribosome map was used as initial reference and then resulting 18 A map from reconstruction of 70S chloro-ribosome was used as a reference for iterative refinement
Magnification calibration50,760
MethodThe projection matching procedure within the SPIDER software was used to get 3D map
Resolution9.4 A
3D fitting
MethodCross-Correlation based manual fitting in 'O'
Refinement ProtocolRigid Body
Refinement SpaceREAL
Target criteriaBest visual fit using the program O
3D fitting list
3D Fitting ID1
PDB entry ID2XYZ and 2ZXY for small and large subunit respectively
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms51118
Nucleic acid atoms31745
Protein atoms19373
Download
PDB format
Allpdb3bbn.ent.gz
pdb3bbn.ent (uncompressed file)
Header onlypdb3bbn.ent.gz
mmCIF format
mmCIF3bbn.cif.gz
XML format
All3bbn.xml.gz
No-atom3bbn-noatom.xml.gz
Ext-atom3bbn-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.8 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.8 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.8 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.8 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB