3DEG

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation

Connell, S.R.Topf, M.Qin, Y.Wilson, D.N.Mielke, T.Fucini, P.Nierhaus, K.H.Spahn, C.M.T.

(2008) Nat.Struct.Mol.Biol. 15: 910-915


  • PubMed Abstract: 
  • EF4 (LepA) is an almost universally conserved translational GTPase in eubacteria. It seems to be essential under environmental stress conditions and has previously been shown to back-translocate the tRNAs on the ribosome, thereby reverting the canoni ...

    EF4 (LepA) is an almost universally conserved translational GTPase in eubacteria. It seems to be essential under environmental stress conditions and has previously been shown to back-translocate the tRNAs on the ribosome, thereby reverting the canonical translocation reaction. In the current work, EF4 was directly visualized in the process of back-translocating tRNAs by single-particle cryo-EM. Using flexible fitting methods, we built a model of ribosome-bound EF4 based on the cryo-EM map and a recently published unbound EF4 X-ray structure. The cryo-EM map establishes EF4 as a noncanonical elongation factor that interacts not only with the elongating ribosome, but also with the back-translocated tRNA in the A-site region, which is present in a previously unseen, intermediate state and deviates markedly from the position of a canonical A-tRNA. Our results, therefore, provide insight into the underlying structural principles governing back-translocation.


    Organizational Affiliation

    Institut f├╝r Medizinische Physik und Biophysik, Charite-Universit├Ątsmedizin Berlin, Ziegelstrasse 5-9, 10117-Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
GTP-binding protein lepA
C
545Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: lepA
EC: 3.6.5.n1
Find proteins for P60785 (Escherichia coli (strain K12))
Go to UniProtKB:  P60785
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
D
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
H
141Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 1
MoleculeChainsLengthOrganism
A/L-tRNAA76Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
P-tRNAB77Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
30S RNA helix 8E16Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
30S RNA helix 14F12Escherichia coli
Entity ID: 5
MoleculeChainsLengthOrganism
50S RNA helix 42-44G70Escherichia coli
Entity ID: 6
MoleculeChainsLengthOrganism
50S RNA helix 95I29Escherichia coli
Entity ID: 7
MoleculeChainsLengthOrganism
50S RNA helix 71J18Escherichia coli
Entity ID: 8
MoleculeChainsLengthOrganism
50S RNA helix 92K15Escherichia coli
Small Molecules
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
A
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
A
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
A
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
A
RNA LINKINGC10 H16 N3 O8 PC
2MG
Query on 2MG
A
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
A
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
A
RNA LINKINGC11 H18 N5 O8 PG
YG
Query on YG
A
RNA LINKINGC21 H29 N6 O12 PG
5MU
Query on 5MU
A, B
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
A
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2012-05-30
    Type: Refinement description
  • Version 1.3: 2014-04-16
    Type: Database references
  • Version 1.4: 2019-12-11
    Type: Data collection, Database references, Derived calculations