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Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP

by single particle reconstruction, at 10.9 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1524, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1524, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3deg
TitleComplex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP
DescriptorRNA binding protein/RNA Complex
KeywordsRIBOSOME, ribosome, translation, LepA, EF4, GTP-binding, Membrane, Nucleotide-binding, Antibiotic resistance, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding, Methylation
AuthorsConnell, S.R., Topf, M., Qin, Y., Wilson, D.N., Mielke, T., Fucini, P., Nierhaus, K.H., Spahn, C.M.T.
DateDeposition: 2008-06-10, Release: 2008-08-19
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-1524, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1524, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1524

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Article
Citation - primary
ArticleNat. Struct. Mol. Biol., Vol. 15, Issue 9, Page 910-5, Year 2008
TitleA new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.
AuthorsSean R Connell, Maya Topf, Yan Qin, Daniel N Wilson, Thorsten Mielke, Paola Fucini, Knud H Nierhaus, Christian M T Spahn
Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117-Berlin, Germany.
KeywordsBiological Transport, Active, Escherichia coli (metabolism), Escherichia coli Proteins (chemistry), Guanosine Triphosphate (metabolism, 86-01-1), Hydrolysis, LepA protein, E coli, Macromolecular Substances, Models, Molecular, RNA, Bacterial (chemistry), RNA, Transfer (chemistry, 9014-25-9), Ribosomes (chemistry), Transcriptional Elongation Factors (chemistry)
LinksPubMed: 19172743
Components
ID 1 : A/L-tRNA
Image
DescriptionA/L-tRNA
Typepolyribonucleotide
Formula weight24890.293 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksSequence view
ID 2 : P-tRNA
Image
DescriptionP-tRNA
Typepolyribonucleotide
Formula weight24816.971 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 3 : 30S RNA helix 8
Image
Description30S RNA helix 8
Typepolyribonucleotide
Formula weight5161.180 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 4 : 30S RNA helix 14
Image
Description30S RNA helix 14
Typepolyribonucleotide
Formula weight3827.362 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 5 : 50S RNA helix 42-44
Image
Description50S RNA helix 42-44
Typepolyribonucleotide
Formula weight22580.658 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 6 : 50S RNA helix 95
Image
Description50S RNA helix 95
Typepolyribonucleotide
Formula weight9394.705 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 7 : 50S RNA helix 71
Image
Description50S RNA helix 71
Typepolyribonucleotide
Formula weight5765.491 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 8 : 50S RNA helix 92
Image
Description50S RNA helix 92
Typepolyribonucleotide
Formula weight4745.866 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 9 : GTP-binding protein lepA
Image
DescriptionGTP-binding protein lepA
Typepolypeptide(L)
FragmentEF4
Formula weight60477.324 Da
Number of molecules1
ID9
SourceMethod: Isolated from a genetically manipulated source
Gene: K12, lepA, b2569, JW2553, ID:83333, Escherichia coli
Host: ID:562, Escherichia coli, Bl21(DE3), plasmid
Plasmid name: pET14b
LinksUniProt: P60785, Sequence view
ID 10 : 30S ribosomal protein S12
Image
Description30S ribosomal protein S12
Typepolypeptide(L)
Formula weight13637.070 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:83333
Organism scientific: Escherichia coli
Strain: K12
LinksUniProt: P0A7S3, 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:83333
Organism scientific: Escherichia coli
Strain: K12
LinksUniProt: P0A7J7, Sequence view
Sample
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Detector
TypeKODAK SO163 FILM
Processing
2D projection selection
Software nameSitus, Mod-EM, Flex-EM
3D reconstruction
Resolution10.9 A
3D fitting
Refinement Protocolrigid body and flexible fitting
Software nameSitus, Mod-EM, Flex-EM
3D fitting list
3D Fitting ID1
PDB entry ID2i2p, 2i2t, 3cb4, 1gix, 2j01
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms12950
Nucleic acid atoms6721
Protein atoms6229
Download
PDB format
Allpdb3deg.ent.gz
pdb3deg.ent (uncompressed file)
Header onlypdb3deg.ent.gz
mmCIF format
mmCIF3deg.cif.gz
XML format
All3deg.xml.gz
No-atom3deg-noatom.xml.gz
Ext-atom3deg-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.9 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5 MB