9GUU

30S mRNA delivery complex (consensus)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of mRNA delivery to the bacterial ribosome.

Webster, M.W.Chauvier, A.Rahil, H.Graziadei, A.Charles, K.Miropolskaya, N.Takacs, M.Saint-Andre, C.Rappsilber, J.Walter, N.G.Weixlbaumer, A.

(2024) Science 386: eado8476-eado8476

  • DOI: https://doi.org/10.1126/science.ado8476
  • Primary Citation of Related Structures:  
    9GR1, 9GUP, 9GUQ, 9GUR, 9GUS, 9GUT, 9GUU, 9GUV, 9GUW, 9GUX

  • PubMed Abstract: 

    Protein synthesis begins with the formation of a ribosome-messenger RNA (mRNA) complex. In bacteria, the small ribosomal subunit (30 S ) is recruited to many mRNAs through base pairing with the Shine-Dalgarno (SD) sequence and RNA binding by ribosomal protein bS1. Translation can initiate on nascent mRNAs, and RNA polymerase (RNAP) can promote the recruitment of the pioneering 30 S . Here, we examined 30 S recruitment to nascent mRNAs using cryo-electron microscopy, single-molecule fluorescence colocalization, and in-cell cross-linking mass spectrometry. We show that bS1 delivers the mRNA to the ribosome for SD duplex formation and 30 S activation. Additionally, bS1 and RNAP stimulate translation initiation. Our work provides a mechanistic framework for how the SD duplex, ribosomal proteins, and RNAP cooperate in 30 S recruitment to mRNAs and establish transcription-translation coupling.


  • Organizational Affiliation

    Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch Cedex, France.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1557Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsAssyFb0911JW0894
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3233Escherichia coli K-12Mutation(s): 0 
Gene Names: 
rpsCA5U30_004548A8502_004027ACN81_25500ACU57_20980AW118_24880AWP47_12665B6R15_004073B6R31_004972BANRA_01945BANRA_04324BCB93_004289BE932_15515BER14_25170BG944_001129BGM66_003597BGZ_02594BGZ_04121BJI68_08695BK292_20485BK383_24665BKL28_004547BR158_003786BTB68_004360BTQ06_10670BvCmsKKP061_03026BvCmsSIP010_02681BXT93_05495C0P57_002664C1Q91_004908C2121_004166C2M16_25425C2R31_004629C3F40_19740C9Z68_22615CF22_004853CG704_20890CIG67_10695CQ842_14345CQ842_22325CTR35_003626CV83915_02784D3C88_13310D3G36_23070D4M65_20635D4N09_20235D9D43_22570D9E49_05220D9J61_16715DD762_23610DIV22_15195DNQ45_03820DNX30_25415DS732_24325DTL43_20935DU321_12065E2865_04467E4K51_21555E5H86_24460E6D34_21695EAI46_07540ECs4179EIA08_24020EIZ93_12405EN85_004353EPS76_07150EPS97_20030EWK56_25060ExPECSC038_03644F7F11_22660F7N46_23945F9413_21170F9461_25590F9B07_24620FGAF848_25890FIJ20_21130FJQ40_18370FKO60_25700FOI11_019195FOI11_03985FPI65_20370FPS11_25365FVB16_04935FWK02_12630FZU14_21885G3V95_19910G3W53_21020G4A38_21575G4A47_20845G5603_24650GAI89_24765GAJ12_24655GFY48_21635GGB84_004455GKF66_21610GNW61_16695GNZ05_25920GOP25_22770GP711_23370GP954_00880GP965_04360GP975_01250GP979_01940GQA06_03885GQE86_20145GQM04_10630GQM13_25265GQM21_11295GQN34_23330GQW07_21485GRO95_20750GRW05_09125GRW24_04690GUC01_21245H0O53_20765H0O72_19480HEP30_018700HEP34_004758HHH44_004523HI055_004152HIE29_005199HJQ60_004999HLX92_10010HLZ50_22115HMV95_19670HMW38_23170HV109_02125HV209_14650HVV39_09330HVW04_17470HVW43_18605HVY77_02110I6H00_20860I6H02_12055J0541_004409J5U05_004075JNP96_25370NCTC10082_02827NCTC10089_00490NCTC10429_01082NCTC10764_03851NCTC10767_01504NCTC10974_00537NCTC11126_02758NCTC11181_02726NCTC11341_01901NCTC7922_04054NCTC7927_00539NCTC7928_02529NCTC8009_01498NCTC8179_05929NCTC8333_00477NCTC8500_00322NCTC8621_00496NCTC8622_00518NCTC8959_03273NCTC8960_03058NCTC9001_04242NCTC9045_00553NCTC9075_00712NCTC9077_00592NCTC9081_00905NCTC9117_00744NCTC9702_00525NCTC9706_02725NCTC9962_06785OGM49_22395P6223_003995QDW62_02130RZR61_12955SAMEA3472112_00681SAMEA3752557_01964WR15_19670

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDBWG_2987
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5156Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6131Escherichia coli K-12Mutation(s): 0 
Gene Names: 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7156Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS1589Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1682Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1784Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1875Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1992Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2087Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2171Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA1,541Escherichia coli K-12
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Entity ID: 23
MoleculeChains LengthOrganismImage
tRNA(fmet) P-site77Escherichia coli K-12
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Entity ID: 24
MoleculeChains LengthOrganismImage
mRNA53synthetic construct
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
M
L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union679734
Agence Nationale de la Recherche (ANR)FranceANR-10-LABX-0030-INRT
Agence Nationale de la Recherche (ANR)FranceANR-10-IDEX-0002-02
European Molecular Biology Organization (EMBO)European Union--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM131922
Wellcome TrustUnited Kingdom203149

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Data collection, Database references