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Structural characterization of mRNA-tRNA translocation intermediates (50S ribosome of class 6 of the six classes)

by single particle reconstruction, at 11.5 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-5362, Image by Jmol

#3: With PDB-3j10, PDB-4v6r, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-5362 (with PDB-3j10), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3j14
TitleStructural characterization of mRNA-tRNA translocation intermediates (50S ribosome of class 6 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
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-5362, Image by Jmol

#3: With PDB-3j10, PDB-4v6r, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-5362 (with PDB-3j10), Image by UCSF CHIMERA

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Related Structure Data
Related Entries

EMDB-5362

CiteFit

PDB-3j10

CiteSplit

PDB-4v6r

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. 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 : 5S ribomosomal RNA
Image
Description5S ribomosomal RNA
Typepolyribonucleotide
Formula weight38790.309 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksGenBank: 33357928, Sequence view
ID 2 : 23S ribomosomal RNA
Image
Description23S ribomosomal RNA
Typepolyribonucleotide
Formula weight941814.875 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksGenBank: 33357927, Sequence view
ID 3 : 50S ribosomal protein L1
Image
Description50S ribosomal protein L1
Typepolypeptide(L)
Formula weight24765.834 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:2285
Organism scientific: Sulfolobus acidocaldarius
LinksUniProt: P0A7L0, Sequence view
ID 4 : 50S ribosomal protein L2
Image
Description50S ribosomal protein L2
Typepolypeptide(L)
Formula weight29792.650 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60422, Sequence view
ID 5 : 50S ribosomal protein L3
Image
Description50S ribosomal protein L3
Typepolypeptide(L)
Formula weight22277.709 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60438, Sequence view
ID 6 : 50S ribosomal protein L4
Image
Description50S ribosomal protein L4
Typepolypeptide(L)
Formula weight22121.723 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60723, Sequence view
ID 7 : 50S ribosomal protein L5
Image
Description50S ribosomal protein L5
Typepolypeptide(L)
Formula weight20202.566 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P62399, Sequence view
ID 8 : 50S ribosomal protein L6
Image
Description50S ribosomal protein L6
Typepolypeptide(L)
Formula weight18801.766 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG55, Sequence view
ID 9 : 50S ribosomal protein L9
Image
Description50S ribosomal protein L9
Typepolypeptide(L)
Formula weight15789.174 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R1, Sequence view
ID 10 : 50S ribosomal protein L10
Image
Description50S ribosomal protein L10
Typepolypeptide(L)
Formula weight17605.537 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:2285
Organism scientific: Sulfolobus acidocaldarius
LinksUniProt: P0A7J3, Sequence view
ID 11 : 50S ribosomal protein L11
Image
Description50S ribosomal protein L11
Typepolypeptide(L)
Formula weight14763.286 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7J7, Sequence view
ID 12 : 50S ribosomal protein L13
Image
Description50S ribosomal protein L13
Typepolypeptide(L)
Formula weight16050.749 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AA10, Sequence view
ID 13 : 50S ribosomal protein L14
Image
Description50S ribosomal protein L14
Typepolypeptide(L)
Formula weight13565.172 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY3, Sequence view
ID 14 : 50S ribosomal protein L15
Image
Description50S ribosomal protein L15
Typepolypeptide(L)
Formula weight15008.598 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02413, Sequence view
ID 15 : 50S ribosomal protein L16
Image
Description50S ribosomal protein L16
Typepolypeptide(L)
Formula weight15312.394 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY7, Sequence view
ID 16 : 50S ribosomal protein L17
Image
Description50S ribosomal protein L17
Typepolypeptide(L)
Formula weight14393.774 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG44, Sequence view
ID 17 : 50S ribosomal protein L18
Image
Description50S ribosomal protein L18
Typepolypeptide(L)
Formula weight12794.793 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0C018, Sequence view
ID 18 : 50S ribosomal protein L19
Image
Description50S ribosomal protein L19
Typepolypeptide(L)
Formula weight13028.207 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7K6, Sequence view
ID 19 : 50S ribosomal protein L20
Image
Description50S ribosomal protein L20
Typepolypeptide(L)
Formula weight13396.962 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L3, Sequence view
ID 20 : 50S ribosomal protein L21
Image
Description50S ribosomal protein L21
Typepolypeptide(L)
Formula weight11586.485 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG48, Sequence view
ID 21 : 50S ribosomal protein L22
Image
Description50S ribosomal protein L22
Typepolypeptide(L)
Formula weight12253.464 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P61175, Sequence view
ID 22 : 50S ribosomal protein L23
Image
Description50S ribosomal protein L23
Typepolypeptide(L)
Formula weight11222.270 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADZ0, Sequence view
ID 23 : 50S ribosomal protein L24
Image
Description50S ribosomal protein L24
Typepolypeptide(L)
Formula weight11208.169 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60624, Sequence view
ID 24 : 50S ribosomal protein L25
Image
Description50S ribosomal protein L25
Typepolypeptide(L)
Formula weight10713.566 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P68919, Sequence view
ID 25 : 50S ribosomal protein L27
Image
Description50S ribosomal protein L27
Typepolypeptide(L)
Formula weight9015.426 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L8, Sequence view
ID 26 : 50S ribosomal protein L28
Image
Description50S ribosomal protein L28
Typepolypeptide(L)
Formula weight8896.435 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M2, Sequence view
ID 27 : 50S ribosomal protein L29
Image
Description50S ribosomal protein L29
Typepolypeptide(L)
Formula weight7286.531 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M6, Sequence view
ID 28 : 50S ribosomal protein L30
Image
Description50S ribosomal protein L30
Typepolypeptide(L)
Formula weight6423.682 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG51, Sequence view
ID 29 : 50S ribosomal protein L31
Image
Description50S ribosomal protein L31
Typepolypeptide(L)
Formula weight7887.165 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M9, Sequence view
ID 30 : 50S ribosomal protein L32
Image
Description50S ribosomal protein L32
Typepolypeptide(L)
Formula weight6332.307 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7N4, Sequence view
ID 31 : 50S ribosomal protein L33
Image
Description50S ribosomal protein L33
Typepolypeptide(L)
Formula weight6257.510 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7N9, Sequence view
ID 32 : 50S ribosomal protein L34
Image
Description50S ribosomal protein L34
Typepolypeptide(L)
Formula weight5397.506 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7P5, Sequence view
ID 33 : 50S ribosomal protein L35
Image
Description50S ribosomal protein L35
Typepolypeptide(L)
Formula weight7181.907 Da
Number of molecules1
ID33
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7Q1, Sequence view
ID 34 : 50S ribosomal protein L36
Image
Description50S ribosomal protein L36
Typepolypeptide(L)
Formula weight4377.415 Da
Number of molecules1
ID34
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7Q6, 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 A and P site tRNAs
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 particles37000
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 particles37000
Resolution11.5 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 ID2I2V
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms94789
Nucleic acid atoms64917
Protein atoms29872
Download
PDB format
Allpdb3j14.ent.gz
pdb3j14.ent (uncompressed file)
Header onlypdb3j14.ent.gz
mmCIF format
mmCIF3j14.cif.gz
XML format
All3j14.xml.gz
No-atom3j14-noatom.xml.gz
Ext-atom3j14-extatom.xml.gz
Movie files
movie #1
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movie #2
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movie #3
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movie #4
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