6O9K

70S initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 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: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
218Escherichia coli 909945-2Mutation(s): 0 
Gene Names: rpsB
Find proteins for U9ZNW8 (Escherichia coli 909945-2)
Go to UniProtKB:  U9ZNW8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
206Escherichia coliMutation(s): 0 
Gene Names: rpsC
Find proteins for A0A376HTV6 (Escherichia coli)
Go to UniProtKB:  A0A376HTV6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
205Escherichia coli KTE75Mutation(s): 0 
Gene Names: rpsD
Find proteins for L3PZ69 (Escherichia coli KTE75)
Go to UniProtKB:  L3PZ69
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
150Escherichia coli (strain SE11)Mutation(s): 0 
Gene Names: rpsE
Find proteins for B6I217 (Escherichia coli (strain SE11))
Go to UniProtKB:  B6I217
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
100Escherichia coli KTE64Mutation(s): 0 
Gene Names: rpsF
Find proteins for S1CG62 (Escherichia coli KTE64)
Go to UniProtKB:  S1CG62
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
151Escherichia coli KTE64Mutation(s): 0 
Gene Names: rpsG
Find proteins for S1D5F0 (Escherichia coli KTE64)
Go to UniProtKB:  S1D5F0
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
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: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
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: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
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: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
117Escherichia coli (strain K12)Mutation(s): 0 
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 99.0741Mutation(s): 0 
Gene Names: rpsL
Find proteins for V6FZ95 (Escherichia coli 99.0741)
Go to UniProtKB:  V6FZ95
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
114Escherichia coli H420Mutation(s): 0 
Gene Names: rpsM
Find proteins for A0A1X3KX08 (Escherichia coli H420)
Go to UniProtKB:  A0A1X3KX08
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
n
61Escherichia coliMutation(s): 0 
Gene Names: rpsN
Find proteins for A0A090BZT4 (Escherichia coli)
Go to UniProtKB:  A0A090BZT4
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
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: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
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: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
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: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
54Escherichia coli KTE193Mutation(s): 0 
Gene Names: rpsR
Find proteins for L3BXG0 (Escherichia coli KTE193)
Go to UniProtKB:  L3BXG0
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
79Escherichia coli H736Mutation(s): 0 
Gene Names: rpsS
Find proteins for F4SQ43 (Escherichia coli H736)
Go to UniProtKB:  F4SQ43
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
85Escherichia coli HVH 87Mutation(s): 0 
Gene Names: rpsT
Find proteins for T6N332 (Escherichia coli HVH 87)
Go to UniProtKB:  T6N332
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
51Escherichia coliMutation(s): 0 
Gene Names: rpsU
Find proteins for A0A0K5Z365 (Escherichia coli)
Go to UniProtKB:  A0A0K5Z365
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-2
z
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: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplD
Find proteins for D7Z9F6 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9F6
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
177Escherichia coli 908573Mutation(s): 0 
Gene Names: rplE
Find proteins for V0YP03 (Escherichia coli 908573)
Go to UniProtKB:  V0YP03
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
G
117Escherichia coli M056Mutation(s): 0 
Gene Names: rplJ
Find proteins for A0A1X3HYZ2 (Escherichia coli M056)
Go to UniProtKB:  A0A1X3HYZ2
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
H
176Escherichia coli KTE10Mutation(s): 0 
Gene Names: rplF
Find proteins for L2VF14 (Escherichia coli KTE10)
Go to UniProtKB:  L2VF14
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
141Escherichia coli PCN033Mutation(s): 0 
Gene Names: rplK
Find proteins for A0A0G3K9Z8 (Escherichia coli PCN033)
Go to UniProtKB:  A0A0G3K9Z8
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplM
Find proteins for D7ZET0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZET0
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
122Escherichia coli H386Mutation(s): 0 
Gene Names: rplN
Find proteins for A0A1X3JBQ6 (Escherichia coli H386)
Go to UniProtKB:  A0A1X3JBQ6
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
143Escherichia coliMutation(s): 0 
Gene Names: rplO
Find proteins for A0A037Y8L6 (Escherichia coli)
Go to UniProtKB:  A0A037Y8L6
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
120Escherichia coli DEC2CMutation(s): 0 
Gene Names: rplQ
Find proteins for H4KMQ6 (Escherichia coli DEC2C)
Go to UniProtKB:  H4KMQ6
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
116N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
114Escherichia coli chi7122Mutation(s): 0 
Gene Names: rplS
Find proteins for J7R4G2 (Escherichia coli chi7122)
Go to UniProtKB:  J7R4G2
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117Escherichia coli KTE73Mutation(s): 0 
Gene Names: rplT
Find proteins for S1EK76 (Escherichia coli KTE73)
Go to UniProtKB:  S1EK76
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplU
Find proteins for D7ZEN7 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZEN7
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplV
Find proteins for D7Z9G0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G0
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
93Escherichia coli O26:H11Mutation(s): 0 
Gene Names: rplW
Find proteins for A0A0A8UEU4 (Escherichia coli O26:H11)
Go to UniProtKB:  A0A0A8UEU4
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
102Escherichia coli PCN033Mutation(s): 0 
Gene Names: rplX
Find proteins for A0A0G3K7Z5 (Escherichia coli PCN033)
Go to UniProtKB:  A0A0G3K7Z5
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coli MS 84-1Mutation(s): 0 
Gene Names: rplY
Find proteins for D7XH79 (Escherichia coli MS 84-1)
Go to UniProtKB:  D7XH79
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
Y
38Escherichia coli (strain UMEA 3162-1)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1))
Go to UniProtKB:  A0A0E2L017
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
0
79Escherichia coli B185Mutation(s): 0 
Gene Names: rpmA
Find proteins for D6IE98 (Escherichia coli B185)
Go to UniProtKB:  D6IE98
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
1
77Escherichia coli 53638Mutation(s): 0 
Gene Names: rpmB
Find proteins for A0A0E1TA76 (Escherichia coli 53638)
Go to UniProtKB:  A0A0E1TA76
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
2
63Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpmC
Find proteins for D7Z9G3 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G3
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
3
58Escherichia coli 2-005-03_S4_C2Mutation(s): 0 
Gene Names: rpmD
Find proteins for A0A029IJY9 (Escherichia coli 2-005-03_S4_C2)
Go to UniProtKB:  A0A029IJY9
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
4
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
5
56Escherichia coli 3-373-03_S4_C2Mutation(s): 0 
Gene Names: rpmF
Find proteins for A0A069XK10 (Escherichia coli 3-373-03_S4_C2)
Go to UniProtKB:  A0A069XK10
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
6
50Escherichia coli B088Mutation(s): 0 
Gene Names: rpmG
Find proteins for D6I2Q0 (Escherichia coli B088)
Go to UniProtKB:  D6I2Q0
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
7
46Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmH
Find proteins for B7MGC4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MGC4
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
8
64Escherichia coli 1.2741Mutation(s): 0 
Gene Names: rpmI
Find proteins for I2RJ64 (Escherichia coli 1.2741)
Go to UniProtKB:  I2RJ64
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
9
271Escherichia coli M863Mutation(s): 0 
Gene Names: rplB
Find proteins for E9YV59 (Escherichia coli M863)
Go to UniProtKB:  E9YV59
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAa1539Escherichia coli
Entity ID: 22
MoleculeChainsLengthOrganism
mRNAx6Escherichia coli
Entity ID: 23
MoleculeChainsLengthOrganism
tRNAy77Escherichia coli
Entity ID: 25
MoleculeChainsLengthOrganism
23S rRNAA2854Escherichia coli
Entity ID: 44
MoleculeChainsLengthOrganism
5S rRNAX118Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 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