5IMR

Structure of ribosome bound to cofactor at 5.7 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.7 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

Structure of the GTP Form of Elongation Factor 4 (EF4) Bound to the Ribosome

Kumar, V.Ero, R.Ahmed, T.Goh, K.J.Zhan, Y.Bhushan, S.Gao, Y.G.

(2016) J.Biol.Chem. 291: 12943-12950

  • DOI: 10.1074/jbc.M116.725945
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase factors, along with elongation factor G and BPI-inducible protein A. Although EF4 is highly conserved in bacterial, mitochondrial, and chloroplast genomes, ...

    Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase factors, along with elongation factor G and BPI-inducible protein A. Although EF4 is highly conserved in bacterial, mitochondrial, and chloroplast genomes, its exact biological function remains controversial. Here we present the cryo-EM reconstitution of the GTP form of EF4 bound to the ribosome with P and E site tRNAs at 3.8-Å resolution. Interestingly, our structure reveals an unrotated ribosome rather than a clockwise-rotated ribosome, as observed in the presence of EF4-GDP and P site tRNA. In addition, we also observed a counterclockwise-rotated form of the above complex at 5.7-Å resolution. Taken together, our results shed light on the interactions formed between EF4, the ribosome, and the P site tRNA and illuminate the GTPase activation mechanism at previously unresolved detail.


    Organizational Affiliation

    From the Institute of Molecular and Cell Biology, The Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, 138673 Singapore, the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
F
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
G
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
H
209Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
I
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
J
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
K
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
L
138Thermus aquaticusGene Names: rpsH
Find proteins for A0A0M9AFS9 (Thermus aquaticus)
Go to UniProtKB:  A0A0M9AFS9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
M
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
N
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
O
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
P
132Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
Q
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
R
61Thermus aquaticusGene Names: rpsZ (rpsN)
Find proteins for A0A0N0BLP2 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLP2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
S
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
T
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
U
105Thermus thermophilusGene Names: rpsQ (rps17)
Find proteins for P24321 (Thermus thermophilus)
Go to UniProtKB:  P24321
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
V
88Thermus thermophilusGene Names: rpsR (rps18)
Find proteins for P80382 (Thermus thermophilus)
Go to UniProtKB:  P80382
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
W
93Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
X
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
Y
27Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Elongation factor 4
C
610Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: lepA
EC: 3.6.5.n1
Find proteins for Q5SKA7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKA7
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
Z
229Thermus thermophilusGene Names: rplA (rpl1)
Find proteins for P27150 (Thermus thermophilus)
Go to UniProtKB:  P27150
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
a
276Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60405
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
b
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplC
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN8
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
c
210Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
d
182Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ0
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
e
180Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplF
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY8
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
f
140Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplM
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60488
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
g
122Thermus thermophilusGene Names: rplN (rpl14)
Find proteins for P60558 (Thermus thermophilus)
Go to UniProtKB:  P60558
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
h
150Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplO
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ7
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
i
141Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60489
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
j
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9Z9H5
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
k
112Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplR
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ4
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
l
146Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60490
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
m
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplT
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60491
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
n
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplU
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60492
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
o
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
p
96Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplW
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP0
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
q
110Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplX
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP9
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
r
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplY (rpl25, rptL5)
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHZ1
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
s
85Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
t
67Thermus thermophilusGene Names: rpmC (rpl29)
Find proteins for Q9LCY4 (Thermus thermophilus)
Go to UniProtKB:  Q9LCY4
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
u
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ6
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
v
71Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmE
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJE1
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
w
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
x
54Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmG (rpl33)
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P35871
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
y
49Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
z
65Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmI
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKU1
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
1
37Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmJ
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHR2
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
2
173Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplJ
Find proteins for Q8VVE3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8VVE3
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
3
147Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplK
Find proteins for Q5SLP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP6
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1522Thermus thermophilus HB8
Entity ID: 23
MoleculeChainsLengthOrganism
23S ribosomal RNAD2893Thermus thermophilus HB8
Entity ID: 24
MoleculeChainsLengthOrganism
5S ribosomal RNAE123Thermus thermophilus HB8
Entity ID: 55
MoleculeChainsLengthOrganism
P site- tRNA477Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389
Entity ID: 56
MoleculeChainsLengthOrganism
E site- tRNA576Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

Download SDF File 
Download CCD File 
C
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Singapore National Research FoundationSingaporeNRF-RF2009- RF001-267

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Other
  • Version 1.2: 2016-06-01
    Type: Other
  • Version 1.3: 2016-06-22
    Type: Structure summary
  • Version 1.4: 2016-06-29
    Type: Database references
  • Version 1.5: 2017-09-27
    Type: Data collection, Database references, Derived calculations