6O7K

30S initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 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

Late steps in bacterial translation initiation visualized using time-resolved cryo-EM.

Kaledhonkar, S.Fu, Z.Caban, K.Li, W.Chen, B.Sun, M.Gonzalez Jr., R.L.Frank, J.

(2019) Nature 570: 400-404

  • DOI: 10.1038/s41586-019-1249-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNA <sup>fMet </sup>)-containing 30S ribosomal initiation complex to form a 70S initiation complex, which ...

    The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNA fMet )-containing 30S ribosomal initiation complex to form a 70S initiation complex, which subsequently matures into a 70S elongation-competent complex. Rapid and accurate formation of the 70S initiation complex is promoted by initiation factors, which must dissociate from the 30S initiation complex before the resulting 70S elongation-competent complex can begin the elongation of translation 1 . Although comparisons of the structures of the 30S 2-5 and 70S 4,6-8 initiation complexes have revealed that the ribosome, initiation factors and fMet-tRNA fMet can acquire different conformations in these complexes, the timing of conformational changes during formation of the 70S initiation complex, the structures of any intermediates formed during these rearrangements, and the contributions that these dynamics might make to the mechanism and regulation of initiation remain unknown. Moreover, the absence of a structure of the 70S elongation-competent complex formed via an initiation-factor-catalysed reaction has precluded an understanding of the rearrangements to the ribosome, initiation factors and fMet-tRNA fMet that occur during maturation of a 70S initiation complex into a 70S elongation-competent complex. Here, using time-resolved cryogenic electron microscopy 9 , we report the near-atomic-resolution view of how a time-ordered series of conformational changes drive and regulate subunit joining, initiation factor dissociation and fMet-tRNA fMet positioning during formation of the 70S elongation-competent complex. Our results demonstrate the power of time-resolved cryogenic electron microscopy to determine how a time-ordered series of conformational changes contribute to the mechanism and regulation of one of the most fundamental processes in biology.


    Organizational Affiliation

    Integrated Program in Cellular, Molecular and Biophysical Studies, Columbia University, College of Physicians and Surgeons, New York, NY, USA.,Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Chemistry, Columbia University, New York, NY, USA. rlg2118@columbia.edu.,Department of Chemistry, Columbia University, New York, NY, USA.,Department of Biological Sciences, Columbia University, New York, NY, USA.,Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA. jf2192@cumc.columbia.edu.,Department of Biological Sciences, Columbia University, New York, NY, USA. jf2192@cumc.columbia.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-1
5
71N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-2
f
509Escherichia coli 3-373-03_S4_C2Mutation(s): 0 
Gene Names: infB
Find proteins for A0A069XYI1 (Escherichia coli 3-373-03_S4_C2)
Go to UniProtKB:  A0A069XYI1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
P
80Escherichia coli 1-250-04_S3_C2Mutation(s): 0 
Gene Names: rpsQ
Find proteins for A0A080IK26 (Escherichia coli 1-250-04_S3_C2)
Go to UniProtKB:  A0A080IK26
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
r
98Escherichia coli MS 198-1Mutation(s): 0 
Gene Names: rpsJ
Find proteins for D7X302 (Escherichia coli MS 198-1)
Go to UniProtKB:  D7X302
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
q
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
t
123Escherichia coli 99.0741Mutation(s): 0 
Gene Names: rpsL
Find proteins for V6FZ95 (Escherichia coli 99.0741)
Go to UniProtKB:  V6FZ95
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
s
114Escherichia coli H420Mutation(s): 0 
Gene Names: rpsM
Find proteins for A0A1X3KX08 (Escherichia coli H420)
Go to UniProtKB:  A0A1X3KX08
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
w
100Escherichia coliMutation(s): 0 
Gene Names: rpsN
Find proteins for A0A090BZT4 (Escherichia coli)
Go to UniProtKB:  A0A090BZT4
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
u
88Escherichia coli MS 84-1Mutation(s): 0 
Gene Names: rpsO
Find proteins for D7XN21 (Escherichia coli MS 84-1)
Go to UniProtKB:  D7XN21
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
y
82Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsP
Find proteins for B7MIU7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIU7
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
1
55Escherichia coli KTE193Mutation(s): 0 
Gene Names: rpsR
Find proteins for L3BXG0 (Escherichia coli KTE193)
Go to UniProtKB:  L3BXG0
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
z
79Escherichia coli H736Mutation(s): 0 
Gene Names: rpsS
Find proteins for F4SQ43 (Escherichia coli H736)
Go to UniProtKB:  F4SQ43
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
j
218Escherichia coli 909945-2Mutation(s): 0 
Gene Names: rpsB
Find proteins for U9ZNW8 (Escherichia coli 909945-2)
Go to UniProtKB:  U9ZNW8
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
3
85Escherichia coli HVH 87Mutation(s): 0 
Gene Names: rpsT
Find proteins for T6N332 (Escherichia coli HVH 87)
Go to UniProtKB:  T6N332
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
2
51Escherichia coliMutation(s): 0 
Gene Names: rpsU
Find proteins for A0A0K5Z365 (Escherichia coli)
Go to UniProtKB:  A0A0K5Z365
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
h
206Escherichia coliMutation(s): 0 
Gene Names: rpsC
Find proteins for A0A376HTV6 (Escherichia coli)
Go to UniProtKB:  A0A376HTV6
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
l
205Escherichia coli KTE75Mutation(s): 0 
Gene Names: rpsD
Find proteins for L3PZ69 (Escherichia coli KTE75)
Go to UniProtKB:  L3PZ69
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
k
150Escherichia coli (strain SE11)Mutation(s): 0 
Gene Names: rpsE
Find proteins for B6I217 (Escherichia coli (strain SE11))
Go to UniProtKB:  B6I217
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
n
100Escherichia coli KTE64Mutation(s): 0 
Gene Names: rpsF
Find proteins for S1CG62 (Escherichia coli KTE64)
Go to UniProtKB:  S1CG62
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
m
151Escherichia coli KTE64Mutation(s): 0 
Gene Names: rpsG
Find proteins for S1D5F0 (Escherichia coli KTE64)
Go to UniProtKB:  S1D5F0
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
p
129Escherichia coli (strain MS 21-1)Mutation(s): 0 
Gene Names: rpsH
Find proteins for D8A1L7 (Escherichia coli (strain MS 21-1))
Go to UniProtKB:  D8A1L7
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
o
127Escherichia coli UMEA 3718-1Mutation(s): 0 
Gene Names: rpsI
Find proteins for T9TH92 (Escherichia coli UMEA 3718-1)
Go to UniProtKB:  T9TH92
Entity ID: 3
MoleculeChainsLengthOrganism
16Sg1539Escherichia coli
Entity ID: 24
MoleculeChainsLengthOrganism
tRNAv77Escherichia coli
Entity ID: 25
MoleculeChainsLengthOrganism
mRNAN6Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01 GM29169
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01 GM55440
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01 GM 084288
American Cancer SocietyUnited States125201

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-07-03
    Type: Data collection, Database references