9H9H | pdb_00009h9h

Complex 1 30S-IF1-IF2-IF3-GE81112

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

A binding site for the antibiotic GE81112 in the ribosomal mRNA channel.

Schedlbauer, A., Han, X., van Bakel, W., Kaminishi, T., Ochoa-Lizarralde, B., Iturrioz, I., Capuni, R., Parry, R., Zegarra, R., Gil-Carton, D., Lopez-Alonso, J.P., Barragan Sanz, K., Brandi, L., Gualerzi, C.O., Fucini, P., Connell, S.R.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.09.26.614503
  • Primary Citation of Related Structures:  
    9H8G, 9H9H, 9H9I, 9H9J, 9H9K, 9H9L, 9H9M, 9H9N

  • PubMed Abstract: 

    The initiation phase is the rate-limiting step of protein synthesis (translation) and is finely regulated, making it an important drug target. In bacteria, initiation is guided by three initiation factors and involves positioning the start site on the messenger RNA within the P-site on the small ribosomal subunit (30S), where it is decoded by the initiator tRNA. This process can be efficiently inhibited by GE81112, a natural hydrophilic, noncyclic, nonribosomal tetrapeptide. It is found in nature in three structural variants (A, B and B1 with molecular masses of 643-658 Da). Previous biochemical and structural characterisation of GE81112 indicates that the primary mechanism of action of this antibiotic is to (1) prevent the initiator tRNA from binding correctly to the P-site and (2) block conformational rearrangements in initiation factor IF3, resulting in an unlocked 30S pre/C state. In this study, using cryoEM, we have determined the binding site of GE81112 in initiation complexes (3.2-3.7Å) and on empty ribosomes (2.09 Å). This binding site is within the mRNA channel (E-site) but remote from the binding site of the initiation factors and initiator tRNA. This suggests that it acts allosterically to prevent the initiator tRNA from being locked into place. The binding mode is consistent with previous biochemical studies and recent work identifying the key pharmacophores of GE81112.

    • Organizational Affiliation: 
    • Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain.

Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2D [auth B]241Escherichia coliMutation(s): 0 
Gene Names: rpsB, b0169, JW0164
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3E [auth C]233Escherichia coliMutation(s): 0 
Gene Names: rpsC, b3314, JW3276
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4F [auth D]206Escherichia coliMutation(s): 0 
Gene Names: rpsD, ramA, b3296, JW3258
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5G [auth E]167Escherichia coliMutation(s): 0 
Gene Names: rpsE, spc, b3303, JW3265
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6, fully modified isoformH [auth F]135Escherichia coliMutation(s): 0 
Gene Names: rpsF, b4200, JW4158
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7I [auth G]179Escherichia coliMutation(s): 0 
Gene Names: rpsG, b3341, JW3303
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8J [auth H]130Escherichia coliMutation(s): 0 
Gene Names: rpsH, b3306, JW3268
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9K [auth I]130Escherichia coliMutation(s): 0 
Gene Names: rpsI, b3230, JW3199
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10L [auth J]103Escherichia coliMutation(s): 0 
Gene Names: rpsJ, nusE, b3321, JW3283
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11M [auth K]129Escherichia coliMutation(s): 0 
Gene Names: rpsK, b3297, JW3259
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12N [auth L]124Escherichia coliMutation(s): 0 
Gene Names: rpsL, strA, b3342, JW3304
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13O [auth M]118Escherichia coliMutation(s): 0 
Gene Names: rpsM, b3298, JW3260
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14P [auth N]101Escherichia coliMutation(s): 0 
Gene Names: rpsN, b3307, JW3269
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15Q [auth O]89Escherichia coliMutation(s): 0 
Gene Names: rpsO, secC, b3165, JW3134
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16R [auth P]82Escherichia coliMutation(s): 0 
Gene Names: rpsP, b2609, JW2590
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17S [auth Q]84Escherichia coliMutation(s): 0 
Gene Names: rpsQ, neaA, b3311, JW3273
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18T [auth R]75Escherichia coliMutation(s): 0 
Gene Names: rpsR, b4202, JW4160
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19U [auth S]92Escherichia coliMutation(s): 0 
Gene Names: rpsS, b3316, JW3278
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20V [auth T]87Escherichia coliMutation(s): 0 
Gene Names: rpsT, b0023, JW0022
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21W [auth U]71Escherichia coliMutation(s): 0 
Gene Names: rpsU, b3065, JW3037
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-172Escherichia coliMutation(s): 0 
Gene Names: infA, b0884, JW0867
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-2890Escherichia coliMutation(s): 0 
Gene Names: infB, EcE24377A_3652
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-3180Escherichia coliMutation(s): 0 
Gene Names: infC, fit, srjA, b1718, JW5829
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Entity ID: 1
MoleculeChains LengthOrganismImage
mRNA (5'-R(P*AP*AP*UP*G)-3')A [auth 2]4Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
t-RNA (77-MER)B [auth 3]77Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
16S RNA (1534-MER)C [auth A]1,542Escherichia coli
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IC4 (Subject of Investigation/LOI)
Query on A1IC4
Download Ideal Coordinates CCD File 
EA [auth A](2S,3S)-2-[[(2S)-2-[[(2S,4S)-5-aminocarbonyloxy-4-oxidanyl-2-[[(2S,3R)-3-oxidanylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-3-(1H-imidazol-4-yl)propanoyl]amino]-3-(2-chloranyl-1H-imidazol-4-yl)-3-oxidanyl-propanoic acid
C24 H34 Cl N9 O10
MPRVLYUMDIXCGD-XYYQMEIKSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
BG [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
AA [auth 2],
AG [auth A],
XF [auth A],
YF [auth A],
ZF [auth A]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
BA [auth 3],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
CA [auth 3],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth K],
DA [auth 3],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2021-122705OB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release