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Structural characterization of mRNA-tRNA translocation intermediates (30S ribosome of class 3 of the six classes)

by single particle reconstruction, at 13.1 A resolution

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#2: Superimposing with simplified surface model of EM map, EMDB-5360, Image by Jmol

#3: With PDB-3j11, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-5360 (with PDB-3j11), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3j13
TitleStructural characterization of mRNA-tRNA translocation intermediates (30S ribosome of class 3 of the six classes)
DescriptorProtein/RNA complex (ribosomal)
KeywordsRIBOSOME, cryoelectron microscopy, molecular dynamics flexible fitting, ratchet-like rotation
AuthorsAgirrezabala, X., Liao, H., Schreiner, E., Fu, J., Ortiz-Meoz, R.F., Schulten, K., Green, R., Frank, J.
DateDeposition: 2011-12-09, Release: 2012-03-21
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-5360, Image by Jmol

#3: With PDB-3j11, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-5360 (with PDB-3j11), Image by UCSF CHIMERA

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EMDB-5360

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PDB-3j11

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Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 109, Issue 16, Page 6094-9, Year 2012
TitleStructural characterization of mRNA-tRNA translocation intermediates.
AuthorsXabier Agirrezabala, Hstau Y Liao, Eduard Schreiner, Jie Fu, Rodrigo F Ortiz-Meoz, Klaus Schulten, Rachel Green, Joachim Frank
Structural Biology Unit, CIC-bioGUNE, Bizkaia Technology Park, Derio 48160, Basque Country, Spain.
KeywordsBinding Sites, Cryoelectron Microscopy, Crystallography, X-Ray, Escherichia coli (genetics), Macromolecular Substances (chemistry), Models, Molecular, Molecular Conformation, Protein Biosynthesis, RNA, Messenger (genetics), RNA, Transfer (genetics, 9014-25-9), Ribosomes (metabolism), Thermodynamics
LinksDOI: 10.1073/pnas.1201288109, PubMed: 22467828, PMC: PMC3340995
Components
ID 1 : 16S ribosomal RNA
Image
Description16S ribosomal RNA
Typepolyribonucleotide
Formula weight499875.594 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksGenBank: 83754040, Sequence view
ID 2 : mRNA
Image
DescriptionmRNA
Typepolyribonucleotide
Formula weight15036.932 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 3 : P site tRNA
Image
DescriptionP site tRNA
Typepolyribonucleotide
Formula weight24833.076 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 4 : 30S ribosomal protein S2
Image
Description30S ribosomal protein S2
Typepolypeptide(L)
Formula weight26650.656 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V0, Sequence view
ID 5 : 30S ribosomal protein S3
Image
Description30S ribosomal protein S3
Typepolypeptide(L)
Formula weight25900.342 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V3, Sequence view
ID 6 : 30S ribosomal protein S4
Image
Description30S ribosomal protein S4
Typepolypeptide(L)
Formula weight23383.191 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V8, Sequence view
ID 7 : 30S ribosomal protein S5
Image
Description30S ribosomal protein S5
Typepolypeptide(L)
Formula weight17498.340 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7W1, Sequence view
ID 8 : 30S ribosomal protein S6
Image
Description30S ribosomal protein S6
Typepolypeptide(L)
Formula weight15727.645 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02358, Sequence view
ID 9 : 30S ribosomal protein S7
Image
Description30S ribosomal protein S7
Typepolypeptide(L)
Formula weight19924.133 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02359, Sequence view
ID 10 : 30S ribosomal protein S8
Image
Description30S ribosomal protein S8
Typepolypeptide(L)
Formula weight14015.469 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7W7, Sequence view
ID 11 : 30S ribosomal protein S9
Image
Description30S ribosomal protein S9
Typepolypeptide(L)
Formula weight14755.199 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7X3, Sequence view
ID 12 : 30S ribosomal protein S10
Image
Description30S ribosomal protein S10
Typepolypeptide(L)
Formula weight11755.708 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R5, Sequence view
ID 13 : 30S ribosomal protein S11
Image
Description30S ribosomal protein S11
Typepolypeptide(L)
Formula weight13739.899 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R9, Sequence view
ID 14 : 30S ribosomal protein S12
Image
Description30S ribosomal protein S12
Typepolypeptide(L)
Formula weight13637.070 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7S3, Sequence view
ID 15 : 30S ribosomal protein S13
Image
Description30S ribosomal protein S13
Typepolypeptide(L)
Formula weight12997.379 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7S9, Sequence view
ID 16 : 30S ribosomal protein S14
Image
Description30S ribosomal protein S14
Typepolypeptide(L)
Formula weight11475.461 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG59, Sequence view
ID 17 : 30S ribosomal protein S15
Image
Description30S ribosomal protein S15
Typepolypeptide(L)
Formula weight10188.777 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: Q8X9M2, Sequence view
ID 18 : 30S ribosomal protein S16
Image
Description30S ribosomal protein S16
Typepolypeptide(L)
Formula weight9207.662 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7T3, Sequence view
ID 19 : 30S ribosomal protein S17
Image
Description30S ribosomal protein S17
Typepolypeptide(L)
Formula weight9593.380 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG63, Sequence view
ID 20 : 30S ribosomal protein S18
Image
Description30S ribosomal protein S18
Typepolypeptide(L)
Formula weight8874.362 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7T7, Sequence view
ID 21 : 30S ribosomal protein S19
Image
Description30S ribosomal protein S19
Typepolypeptide(L)
Formula weight10324.260 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7U3, Sequence view
ID 22 : 30S ribosomal protein S20
Image
Description30S ribosomal protein S20
Typepolypeptide(L)
Formula weight9577.354 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7U7, Sequence view
ID 23 : 30S ribosomal protein S21
Image
Description30S ribosomal protein S21
Typepolypeptide(L)
Formula weight8392.929 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P68679, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Mass-estimation Method2.8
Theoretical Mass2.8
NameTrp-tRNA-EFTu-GDP-kir-70S ribosome
Num components3
Entity assembly
Assembly-ID1
Detailswith P site tRNA
Name70S ribosome
TypeRIBOSOME
Buffer
NameHiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample concentration0.03 mg/ml
Sample support
Details200 mesh
Grid mesh size200
Vitrification
Cryogen nameNITROGEN
DetailsBlot for 3 seconds, plunge into liquid nitrogen (Vitrobot)
Humidity90
InstrumentVitrobot
Methodblot for 3 seconds
Temp80 Kelvin
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F30
Date2011-05-01
Detailsautomated data collection system AutoEMation (CCD mag. 100000x)
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose25 e/A**2
Illumination modeFLOODBEAM
Lens
ModeBRIGHTFIELD
MagnificationCalibrated: 58269 X, Nominal: 59000 X
CsNominal: 2.26 mm
Nominal defocusMax: 4000 nm, Min: 1200 nm
Energy filternone
Specimen holder
Specimen holderModel: OTHER, Type: cartridge
Temperature80.7 Kelvin
Recording temperatureMaximum: 80.7, Minimum: 80.7
Detector
TypeTVIPS TemCam-F415 (CCD)
Processing
2D projection selection
Number of particles21000
Software nameMDFF
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
Actual pixel size1.5 A/pix
CTF correction methodVolumes were CTF-corrected in defocus groups
Magnification calibration50000
Number of particles21000
Resolution13.1 A
Resolution methodFSC at 0.5 cut-off
SoftwareSPIDER
3D fitting
Refinement ProtocolMolecular Dynamics based flexible fitting
Refinement SpaceREAL
Software nameMDFF
Target criteriaRMSD, cross correlation
3D fitting list
3D Fitting ID1
PDB entry ID2I2U
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms55911
Nucleic acid atoms35723
Protein atoms20188
Download
PDB format
Allpdb3j13.ent.gz
pdb3j13.ent (uncompressed file)
Header onlypdb3j13.ent.gz
mmCIF format
mmCIF3j13.cif.gz
XML format
All3j13.xml.gz
No-atom3j13-noatom.xml.gz
Ext-atom3j13-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), 3.4 MB
.webm (WebM/VP8 format), 4.4 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 3.9 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.4 MB