6AWD

Structure of 30S (S1 depleted) ribosomal subunit and RNA polymerase complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Structure of RNA polymerase bound to ribosomal 30S subunit.

Demo, G.Rasouly, A.Vasilyev, N.Svetlov, V.Loveland, A.B.Diaz-Avalos, R.Grigorieff, N.Nudler, E.Korostelev, A.A.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.28560
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA polymerase (RNAP) and the translational machinery. We pres ...

    In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA polymerase (RNAP) and the translational machinery. We present cryo-EM structures of E. coli RNAP core bound to the small ribosomal 30S subunit. The complex is stable under cell-like ionic conditions, consistent with functional interaction between RNAP and the 30S subunit. The RNA exit tunnel of RNAP aligns with the Shine-Dalgarno-binding site of the 30S subunit. Ribosomal protein S1 forms a wall of the tunnel between RNAP and the 30S subunit, consistent with its role in directing mRNAs onto the ribosome. The nucleic-acid-binding cleft of RNAP samples distinct conformations, suggesting different functional states during transcription-translation coupling. The architecture of the 30S•RNAP complex provides a structural basis for co-localization of the transcriptional and translational machineries, and inform future mechanistic studies of coupled transcription and translation.


    Organizational Affiliation

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
01, 02
229Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for P0A7Z6 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A7Z6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
03
1340Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for B7MIX3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIX3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
04
1369Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for P0A8T8 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A8T8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
05
59Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for B7MFL0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MFL0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
E
218Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsB
Find proteins for B7MBF0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBF0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
F
206Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsC
Find proteins for B7MCS9 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS9
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
G
205Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsD
Find proteins for B7MCR2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR2
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
H
157Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpsE
Find proteins for P0A7W3 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A7W3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
I
100Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)Mutation(s): 0 
Gene Names: rpsF
Find proteins for B7NGD4 (Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC))
Go to UniProtKB:  B7NGD4
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
J
151Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsG
Find proteins for B7MCV6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCV6
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
K
129Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsH
Find proteins for B7MCS1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS1
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
L
127Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsI
Find proteins for B7MBZ1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBZ1
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
M
98Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for B7MCT6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT6
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
N
116Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsK
Find proteins for B7MCR3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
O
123Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsL
Find proteins for B7MCV7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCV7
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
P
114Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7T1 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A7T1
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
Q
100Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsN
Find proteins for B7MCS2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS2
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
R
88Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsO
Find proteins for B7MB86 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MB86
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
S
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: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
T
80Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for B7MCS6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS6
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
U
65Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsR
Find proteins for B7MLK7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MLK7
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
V
79Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsS
Find proteins for B7MCT1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT1
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
W
85Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsT
Find proteins for B7MAE3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MAE3
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
X
65Escherichia coli O9:H4 (strain HS)Mutation(s): 0 
Gene Names: rpsU
Find proteins for A8A4M2 (Escherichia coli O9:H4 (strain HS))
Go to UniProtKB:  A8A4M2
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAA1539Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.1 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 Institute of General Medical SciencesUnited StatesGM106105
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM107465
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM107329

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references
  • Version 2.0: 2017-12-06
    Type: Author supporting evidence, Polymer sequence
  • Version 2.1: 2018-07-18
    Type: Data collection