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Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors

by single particle reconstruction, at 7.3 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1315, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1315, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2om7
TitleStructural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors
DescriptorRNA binding protein/RNA Complex
KeywordsRIBOSOME, RNA-Protein Complex
AuthorsConnell, S.R., Wilson, D.N., Rost, M., Schueler, M., Giesebrecht, J., Dabrowski, M., Mielke, T., Fucini, P., Spahn, C.M.T.
DateDeposition: 2007-01-21, Release: 2008-01-15
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-1315, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1315, Image by UCSF CHIMERA

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EMDB-1315

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Article
Citation - primary
ArticleMol. Cell, Vol. 25, Issue 5, Page 751-64, Year 2007
TitleStructural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
AuthorsSean R Connell, Chie Takemoto, Daniel N Wilson, Hongfei Wang, Kazutaka Murayama, Takaho Terada, Mikako Shirouzu, Maximilian Rost, Martin Schüler, Jan Giesebrecht, Marylena Dabrowski, Thorsten Mielke, Paola Fucini, Shigeyuki Yokoyama, Christian M T Spahn
Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117 Berlin, Germany.
KeywordsBinding Sites, Cryoelectron Microscopy, Crystallography, X-Ray, Guanosine Triphosphate (metabolism, 86-01-1), Guanylyl Imidodiphosphate (metabolism, 34273-04-6), Models, Molecular, Peptide Elongation Factor G (chemistry), Protein Structure, Secondary, Protein Structure, Tertiary, Ribosomes (chemistry), Structure-Activity Relationship, Thermus thermophilus (metabolism)
LinksPII: S1097-2765(07)00050-0, DOI: 10.1016/j.molcel.2007.01.027, PubMed: 17349960
Components
ID 1 : Fragment of 16S rRNA (h14)
Image
DescriptionFragment of 16S rRNA (h14)
Typepolyribonucleotide
Formula weight3827.362 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Details: 16S rRNA
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksSequence view
ID 2 : Fragment of 16S rRNA (h15)
Image
DescriptionFragment of 16S rRNA (h15)
Typepolyribonucleotide
Formula weight9048.513 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Details: 16S rRNA
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksSequence view
ID 3 : Fragment of 16S rRNA (h44)
Image
DescriptionFragment of 16S rRNA (h44)
Typepolyribonucleotide
Formula weight31208.826 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Details: 16S rRNA
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksGenBank: 118505352, Sequence view
ID 4 : 16S ribosomal RNA (H5)
Image
Description16S ribosomal RNA (H5)
Typepolyribonucleotide
Formula weight98293.047 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Details: 16S rRNA
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksGenBank: 48256, Sequence view
ID 5 : Fragment of23S rRNA (H95)
Image
DescriptionFragment of23S rRNA (H95)
Typepolyribonucleotide
Formula weight9378.706 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Details: 23S rRNA
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksSequence view
ID 6 : Fragment of23S rRNA (H68)
Image
DescriptionFragment of23S rRNA (H68)
Typepolyribonucleotide
Formula weight17631.746 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Details: 23S rRNA
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksGenBank: 37223182, Sequence view
ID 7 : Fragment of23S rRNA (H89)
Image
DescriptionFragment of23S rRNA (H89)
Typepolyribonucleotide
Formula weight13540.153 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Details: 23S rRNA
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksSequence view
ID 8 : Fragment of23S rRNA (H42-44)
Image
DescriptionFragment of23S rRNA (H42-44)
Typepolyribonucleotide
Formula weight18710.258 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Details: 23S rRNA
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksGenBank: 37223182, Sequence view
ID 9 : Fragment of23S rRNA (H76)
Image
DescriptionFragment of23S rRNA (H76)
Typepolyribonucleotide
Formula weight33148.875 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Details: 23S rRNA
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksGenBank: 37223182, Sequence view
ID 10 : p/E-tRNA
Image
Descriptionp/E-tRNA
Typepolyribonucleotide
Formula weight23728.281 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Details: tRNA
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksSequence view
ID 11 : 30S ribosomal protein S12
Image
Description30S ribosomal protein S12
Typepolypeptide(L)
Formula weight14920.887 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Details: Small ribosomal subunit protein S12
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksUniProt: P17293, Sequence view
ID 12 : 50S ribosomal protein L1
Image
Description50S ribosomal protein L1
Typepolypeptide(L)
Formula weight24872.914 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Details: Large ribosomal subunit protein L1
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksUniProt: Q5SLP7, Sequence view
ID 13 : EF-G
Image
DescriptionElongation factor G
Typepolypeptide(L)
Formula weight76977.914 Da
Number of molecules1
ID13
SourceMethod: Isolated from a genetically manipulated source
Gene: Thermus, fusA, fus, ID:274, Thermus thermophilus
Host: Escherichia, Escherichia coli

, ID:469008, Escherichia coli BL21(DE3), BL21(DE3)
LinksUniProt: P13551, Sequence view
ID 14 : 30S ribosomal protein S2
Image
Description30S ribosomal protein S2
Typepolypeptide(L)
Formula weight29317.918 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Details: Small ribosomal subunit protein S2
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksUniProt: P80371, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Namecomplex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNP
Entity assembly
Assembly-ID1
GO-IDGO:0015935
InterPro-IDIPR:005679
Name30S ribosomal protein S12
Entity assembly
Assembly-ID1
GO-IDGO:0006412
InterPro-IDIPR:002143
Name50S ribosomal protein L1
Entity assembly
Assembly-ID1
GO-IDGO:0006414
InterPro-IDIPR:004540
NameElongation factor G
Entity assembly
Assembly-ID1
GO-IDGO:0003735
InterPro-IDIPR:001865
Name30S ribosomal protein S2
Buffer
Name0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol
Sample preparation
pH7.8
Vitrification
Cryogen nameETHANE
Humidity95
InstrumentVitrobot
Temp277 Kelvin
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F30
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose19 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationNominal: 39000 X
Nominal defocusMax: 4000 nm, Min: 800 nm
Specimen holder
Specimen holderType: Eucentric
Detector
TypeKodak SO163 film
Processing
2D projection selection
Software nameSPIDER
3D reconstruction
CTF correction methoddefocus groups
DetailsThe geometry of linkages between some residues in chains J, M and L are distorted. They were not resolved based on the data used for solving this structure.
Resolution7.3 A
3D fitting
MethodRigid Body
Software nameSitus
3D fitting list
3D Fitting ID1
PDB entry ID2j00, 1gix, 2j01, 1FNM, 1YL3,
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms19031
Nucleic acid atoms9891
Protein atoms9140
Software
Ordinal1
Classificationrefinement
NameSPIDER
Download
PDB format
Allpdb2om7.ent.gz
pdb2om7.ent (uncompressed file)
Header onlypdb2om7.ent.gz
mmCIF format
mmCIF2om7.cif.gz
XML format
All2om7.xml.gz
No-atom2om7-noatom.xml.gz
Ext-atom2om7-extatom.xml.gz
Movie files
movie #1
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.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.6 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.4 MB