3JCE

Structure of Escherichia coli EF4 in pretranslocational ribosomes (Pre EF4)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome

Zhang, D.Yan, K.Liu, G.Song, G.Luo, J.Shi, Y.Cheng, E.Wu, S.Jiang, T.Lou, J.Gao, N.Qin, Y.

(2016) Nat Struct Mol Biol 23: 125-131

  • DOI: 10.1038/nsmb.3160
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2-Å resolution, respectively. In Post-EF4, peptidyl-t ...

    EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2-Å resolution, respectively. In Post-EF4, peptidyl-tRNA occupies the peptidyl (P) site, but the interaction between its CCA end and the P loop is disrupted. In Pre-EF4, the peptidyl-tRNA assumes a unique position near the aminoacyl (A) site, denoted the A site/EF4 bound (A/4) site, with a large displacement at its acceptor arm. Mutagenesis analyses suggest that a specific region in the EF4 C-terminal domain (CTD) interferes with base-pairing between the peptidyl-tRNA 3'-CCA and the P loop, whereas the EF4 CTD enhances peptidyl-tRNA interaction at the A/4 site. Therefore, EF4 induces back-translocation by disengaging the tRNA's CCA end from the peptidyl transferase center of the translating ribosome.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
130Escherichia coli K-12Mutation(s): 0 
Gene Names: b3230JW3199rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
129Escherichia coli K-12Mutation(s): 0 
Gene Names: b3297JW3259rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9

Find similar proteins by: Sequence  |  Structure

Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4

Find similar proteins by: Sequence  |  Structure

Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3

Find similar proteins by: Sequence  |  Structure

Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7

Find similar proteins by: Sequence  |  Structure

Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
92Escherichia coli K-12Mutation(s): 0 
Gene Names: b3316JW3278rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3

Find similar proteins by: Sequence  |  Structure

Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679

Find similar proteins by: Sequence  |  Structure

Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0

Find similar proteins by: Sequence  |  Structure

Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4

Find similar proteins by: Sequence  |  Structure

Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5

Find similar proteins by: Sequence  |  Structure

Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422

Find similar proteins by: Sequence  |  Structure

Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438

Find similar proteins by: Sequence  |  Structure

Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399

Find similar proteins by: Sequence  |  Structure

Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55

Find similar proteins by: Sequence  |  Structure

Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1

Find similar proteins by: Sequence  |  Structure

Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
142Escherichia coli K-12Mutation(s): 0 
Gene Names: b3983JW3946relCrplK
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7

Find similar proteins by: Sequence  |  Structure

Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10

Find similar proteins by: Sequence  |  Structure

Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7

Find similar proteins by: Sequence  |  Structure

Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018

Find similar proteins by: Sequence  |  Structure

Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6

Find similar proteins by: Sequence  |  Structure

Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
100Escherichia coli K-12Mutation(s): 0 
Gene Names: b3318JW3280rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0

Find similar proteins by: Sequence  |  Structure

Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624

Find similar proteins by: Sequence  |  Structure

Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919

Find similar proteins by: Sequence  |  Structure

Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2

Find similar proteins by: Sequence  |  Structure

Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51

Find similar proteins by: Sequence  |  Structure

Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3

Find similar proteins by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9

Find similar proteins by: Sequence  |  Structure

Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
n
101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59

Find similar proteins by: Sequence  |  Structure

Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63

Find similar proteins by: Sequence  |  Structure

Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3

Find similar proteins by: Sequence  |  Structure

Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9

Find similar proteins by: Sequence  |  Structure

Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1

Find similar proteins by: Sequence  |  Structure

Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6

Find similar proteins by: Sequence  |  Structure

Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
5
234Escherichia coli K-12Mutation(s): 0 
Gene Names: rplAb3984JW3947
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L0

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8

Find similar proteins by: Sequence  |  Structure

Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723

Find similar proteins by: Sequence  |  Structure

Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3

Find similar proteins by: Sequence  |  Structure

Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1

Find similar proteins by: Sequence  |  Structure

Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44

Find similar proteins by: Sequence  |  Structure

Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3

Find similar proteins by: Sequence  |  Structure

Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48

Find similar proteins by: Sequence  |  Structure

Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175

Find similar proteins by: Sequence  |  Structure

Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8

Find similar proteins by: Sequence  |  Structure

Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6

Find similar proteins by: Sequence  |  Structure

Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
Elongation factor 4
x
599Escherichia coli K-12Mutation(s): 0 
Gene Names: lepAb2569JW2553
EC: 3.6.5.1 (PDB Primary Data), 3.6.5 (UniProt)
Find proteins for P60785 (Escherichia coli (strain K12))
Go to UniProtKB:  P60785

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
130Escherichia coli K-12Mutation(s): 0 
Gene Names: b3306JW3268rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAa1533Escherichia coli K-12

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 28
MoleculeChainsLengthOrganism
23 ribosomal RNAA2904Escherichia coli K-12

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 29
MoleculeChainsLengthOrganism
5S ribosomal RNAB120Escherichia coli K-12

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 54
MoleculeChainsLengthOrganism
tRNA676synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 55
MoleculeChainsLengthOrganism
mRNA715synthetic construct

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 58
MoleculeChainsLengthOrganism
tRNA976synthetic construct

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 56
MoleculeChainsLengthOrganism
tRNA877synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download CCD File 
x
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
x
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references
  • Version 1.2: 2016-04-20
    Changes: Structure summary
  • Version 1.3: 2017-02-22
    Changes: Database references
  • Version 1.4: 2019-12-11
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 2.0: 2019-12-18
    Changes: Advisory, Atomic model, Data collection, Derived calculations