4V69

Ternary complex-bound E.coli 70S ribosome.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

Villa, E., Sengupta, J., Trabuco, L.G., LeBarron, J., Baxter, W.T., Shaikh, T.R., Grassucci, R.A., Nissen, P., Ehrenberg, M., Schulten, K., Frank, J.

(2009) Proc Natl Acad Sci U S A 106: 1063-1068

  • DOI: https://doi.org/10.1073/pnas.0811370106
  • Primary Citation of Related Structures:  
    4V69

  • PubMed Abstract: 

    In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-A cryo-electron microscopy map of the aminoacyl-tRNA x EF-Tu x GDP x kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic gate mechanism.

    • Organizational Affiliation: 

    Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10A [auth AJ]98Escherichia coliMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11B [auth AK]117Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12C [auth AL]123Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13D [auth AM]113Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14E [auth AN]96Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15F [auth AO]88Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16G [auth AP]80Escherichia coliMutation(s): 0 
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30S ribosomal protein S17H [auth AQ]80Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18I [auth AR]55Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19J [auth AS]79Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20K [auth AT]85Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21L [auth AU]51Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2M [auth AB]218Escherichia coliMutation(s): 0 
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30S ribosomal protein S3N [auth AC]206Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4O [auth AD]205Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5P [auth AE]150Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6Q [auth AF]100Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7R [auth AG]150Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8S [auth AH]129Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9T [auth AI]127Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor TuY [auth AZ]393Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1AA [auth B5]234Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11BA [auth BI]141Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13CA [auth BJ]142Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14DA [auth BK]121Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15EA [auth BL]143Escherichia coliMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L16FA [auth BM]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17GA [auth BN]120Escherichia coliMutation(s): 0 
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50S ribosomal protein L18HA [auth BO]116Escherichia coliMutation(s): 0 
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50S ribosomal protein L19IA [auth BP]114Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20JA [auth BQ]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L21KA [auth BR]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22LA [auth BS]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23MA [auth BT]93Escherichia coliMutation(s): 0 
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50S ribosomal protein L24NA [auth BU]102Escherichia coliMutation(s): 0 
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50S ribosomal protein L25OA [auth BV]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27PA [auth BW]79Escherichia coliMutation(s): 0 
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50S ribosomal protein L28QA [auth BX]77Escherichia coliMutation(s): 0 
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50S ribosomal protein L29RA [auth BY]63Escherichia coliMutation(s): 0 
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50S ribosomal protein L2SA [auth BC]271Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30TA [auth BZ]58Escherichia coliMutation(s): 0 
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50S ribosomal protein L32UA [auth B0]56Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33VA [auth B1]50Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34WA [auth B2]46Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35XA [auth B3]64Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36YA [auth B4]38Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3ZA [auth BD]209Escherichia coliMutation(s): 0 
UniProt
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UniProt GroupP60438
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4AB [auth BE]201Escherichia coliMutation(s): 0 
UniProt
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UniProt GroupP60723
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5BB [auth BF]178Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6CB [auth BG]176Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9DB [auth BH]149Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains LengthOrganismImage
16S rRNAU [auth AA]1,530Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
A/T-site tRNA PheV [auth AY]76N/A
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Entity ID: 23
MoleculeChains LengthOrganismImage
P-site tRNA fMet (Unmodified bases except for Thymine 54)W [auth AW]76Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
mRNAX [auth AX]11N/A
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Entity ID: 26
MoleculeChains LengthOrganismImage
E-site tRNA PheZ [auth AV]77Escherichia coli
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Entity ID: 57
MoleculeChains LengthOrganismImage
23S ribosomal RNAEB [auth BB]2,903Escherichia coli
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Entity ID: 58
MoleculeChains LengthOrganismImage
5S ribosomal RNAFB [auth BA]117Escherichia coli
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
GB [auth AZ]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-03-25
    Changes: Other
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-18
    Changes: Database references, Derived calculations, Other
  • Version 1.5: 2024-02-28
    Changes: Data collection, Database references, Refinement description