5ME0

Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.5 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

Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways.

Lopez-Alonso, J.P.Fabbretti, A.Kaminishi, T.Iturrioz, I.Brandi, L.Gil-Carton, D.Gualerzi, C.O.Fucini, P.Connell, S.R.

(2017) Nucleic Acids Res. 45: 2179-2187

  • DOI: 10.1093/nar/gkw1251
  • Primary Citation of Related Structures:  5ME1

  • PubMed Abstract: 
  • In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the initiator tRNA in a process guided and controlled by thre ...

    In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the initiator tRNA in a process guided and controlled by three initiation factors. This process can be efficiently inhibited by GE81112, a natural tetrapeptide antibiotic that is highly specific toward bacteria. Here GE81112 was used to stabilize the 30S pre-initiation complex and obtain its structure by cryo-electron microscopy. The results obtained reveal the occurrence of changes in both the ribosome conformation and initiator tRNA position that may play a critical role in controlling translational fidelity. Furthermore, the structure highlights similarities with the early steps of initiation in eukaryotes suggesting that shared structural features guide initiation in all kingdoms of life.


    Organizational Affiliation

    Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
241Escherichia coli (strain K12)Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
C
233Escherichia coli (strain K12)Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
206Escherichia coli (strain K12)Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
E
167Escherichia coli (strain K12)Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
131Escherichia coli (strain K12)Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
G
156Escherichia coli (strain K12)Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
130Escherichia coli (strain K12)Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
I
130Escherichia coli (strain K12)Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J
103Escherichia coli (strain K12)Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
K
129Escherichia coli (strain K12)Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
123Escherichia coli (strain K12)Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
M
118Escherichia coli (strain K12)Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
N
101Escherichia coli (strain K12)Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
89Escherichia coli (strain K12)Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
P
102Escherichia coliGene Names: rpsP
Find proteins for A0A0U4BH30 (Escherichia coli)
Go to UniProtKB:  A0A0U4BH30
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Q
84Escherichia coli (strain K12)Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
R
75Escherichia coli (strain K12)Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
92Escherichia coli (strain K12)Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
T
87Escherichia coli (strain K12)Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
U
71Escherichia coli (strain K12)Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-1
V
72Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: infA
Find proteins for Q5SHR1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHR1
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-2
W
890Escherichia coli (strain K12)Gene Names: infB (gicD, ssyG)
Find proteins for P0A705 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A705
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-3
Y
171Geobacillus stearothermophilusGene Names: infC
Find proteins for P03000 (Geobacillus stearothermophilus)
Go to UniProtKB:  P03000
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-3
Z
144Escherichia coli (strain K12)Gene Names: infC (fit, srjA)
Find proteins for P0A707 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A707
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1534Escherichia coli K-12
Entity ID: 26
MoleculeChainsLengthOrganism
fMet-tRNAX77Escherichia coli K-12
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

Download SDF File 
Download CCD File 
X
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A, X
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
A
RNA LINKINGC10 H16 N3 O8 PC
D2T
Query on D2T
L
L-peptide linkingC5 H9 N O4 SASP
MA6
Query on MA6
A
RNA LINKINGC12 H18 N5 O7 PA
4SU
Query on 4SU
X
RNA LINKINGC9 H13 N2 O8 P SU
2MG
Query on 2MG
A
RNA LINKINGC11 H16 N5 O8 PG
G7M
Query on G7M
A
RNA LINKINGC11 H17 N5 O8 PG
UR3
Query on UR3
A
RNA LINKINGC10 H15 N2 O9 PU
5MU
Query on 5MU
X
RNA LINKINGC10 H15 N2 O9 PU
4OC
Query on 4OC
A
RNA LINKINGC11 H18 N3 O8 PC
H2U
Query on H2U
X
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.5 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
European UnionItalyQLRT- 2001-00892
Marie Curie Actions; COFUNDSpain--
Marie Curie Action Career Integration GrantSpainPCIG14-GA-2013-632072
Spanish Ministry of Economy and CompetitivenessSpainCTQ2014-55907-R

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references
  • Version 1.2: 2017-08-30
    Type: Advisory, Data collection, Derived calculations
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence