4V69

Ternary complex-bound E.coli 70S ribosome.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.USA 106: 1063-1068

  • DOI: 10.1073/pnas.0811370106
  • Primary Citation of Related Structures:  

  • 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 selecti ...

    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.


    Related Citations: 
    • Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
      Trabuco, L.,Villa, E.,Mitra, K.,Frank, J.,Schulten, K.
      (2008) Structure 16: 673
    • Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome
      LeBarron, J.,Grassucci, R.A.,Shaikh, T.R.,Baxter, W.T.,Sengupta, J.,Frank, J.
      (2008) J.Struct.Biol. 164: 24


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ
98Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL
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: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM
113Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN
96Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO
88Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q8X9M2 (Escherichia coli O157:H7)
Go to UniProtKB:  Q8X9M2
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP
80Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ
80Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS
79Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AU
51Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB
218Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD
205Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE
150Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG
150Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu
AZ
393Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tufA
Find proteins for P0CE47 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE47
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
B5
234Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplA
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L0
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BI
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: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BJ
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BK
121Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BL
143Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BM
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BN
120Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BO
116Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BP
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BQ
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BR
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BS
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BT
93Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BU
102Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BV
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BW
79Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BX
77Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
BY
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BC
271Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
BZ
58Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B0
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B1
50Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B2
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B3
64Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B4
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BD
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BE
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BF
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BG
176Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BH
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 21
MoleculeChainsLengthOrganism
16S rRNAAA1530Escherichia coli
Entity ID: 22
MoleculeChainsLengthOrganism
A/T-site tRNA PheAY76N/A
Entity ID: 23
MoleculeChainsLengthOrganism
P-site tRNA fMet (Unmodified bases except for Thymine 54)AW76Escherichia coli
Entity ID: 24
MoleculeChainsLengthOrganism
mRNAAX11N/A
Entity ID: 26
MoleculeChainsLengthOrganism
E-site tRNA PheAV77Escherichia coli
Entity ID: 57
MoleculeChainsLengthOrganism
23S ribosomal RNABB2903Escherichia coli
Entity ID: 58
MoleculeChainsLengthOrganism
5S ribosomal RNABA117Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
AZ
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5MU
Query on 5MU
AV
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.7 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: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2015-03-25
    Type: Other
  • Version 1.3: 2018-07-18
    Type: Data collection