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- PDB-6awb: Structure of 30S ribosomal subunit and RNA polymerase complex in ... -

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Basic information

Entry
Database: PDB / ID: 6awb
TitleStructure of 30S ribosomal subunit and RNA polymerase complex in non-rotated state
Components
  • (30S ribosomal protein ...) x 21
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • 16S rRNA
KeywordsRIBOSOME / 30S subunit RNA polymerase complex
Function / homology
Function and homology information


ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / transcription, DNA-templated ...ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / transcription, DNA-templated / protein dimerization activity / mRNA binding / magnesium ion binding / DNA binding / zinc ion binding
RNA polymerase Rpb2, OB-fold / Ribosomal protein S5, N-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / DNA-directed RNA polymerase, subunit 2 ...RNA polymerase Rpb2, OB-fold / Ribosomal protein S5, N-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, insert domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Translation elongation factor EF1B/ribosomal protein S6 / DNA-directed RNA polymerase, subunit beta-prime / Ribosomal protein S18, conserved site / Nucleic acid-binding, OB-fold / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / RNA polymerase, alpha subunit, C-terminal / Ribosomal protein S13-like, H2TH / DNA-directed RNA polymerase beta subunit, bacterial-type / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / RNA polymerase Rpb2, domain 3 / Ribosomal protein S14, conserved site / Ribosomal protein S21, conserved site / RNA polymerase Rpb2, domain 2 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S3, C-terminal domain superfamily / RPB6/omega subunit-like superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S3, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 7 / RNA polymerase, RBP11-like subunit / Ribosomal protein S17/S11 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S14 / Ribosomal protein S5 / Ribosomal protein S9 / RNA polymerase, alpha subunit / Ribosomal protein S8 / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S16 / Ribosomal protein S5/S7 / RNA polymerase, beta subunit, conserved site / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, funnel domain superfamily / Ribosomal protein S21 superfamily / RNA polymerase Rpb1, domain 3 superfamily / Ribosomal protein S14/S29 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S21 / Ribosomal protein S4/S9, N-terminal / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase, subunit omega/K/RPB6 / Ribosomal protein S12/S23 / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid
30S ribosomal protein S10 / DNA-directed RNA polymerase subunit alpha / 30S ribosomal protein S5 / 30S ribosomal protein S13 / 30S ribosomal protein S6 / 30S ribosomal protein S18 / DNA-directed RNA polymerase subunit beta / 30S ribosomal protein S16 / DNA-directed RNA polymerase subunit omega / 30S ribosomal protein S12 ...30S ribosomal protein S10 / DNA-directed RNA polymerase subunit alpha / 30S ribosomal protein S5 / 30S ribosomal protein S13 / 30S ribosomal protein S6 / 30S ribosomal protein S18 / DNA-directed RNA polymerase subunit beta / 30S ribosomal protein S16 / DNA-directed RNA polymerase subunit omega / 30S ribosomal protein S12 / 30S ribosomal protein S7 / 30S ribosomal protein S11 / 30S ribosomal protein S19 / 30S ribosomal protein S3 / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 30S ribosomal protein S8 / 30S ribosomal protein S4 / 30S ribosomal protein S9 / 30S ribosomal protein S2 / 30S ribosomal protein S15 / 30S ribosomal protein S20 / 30S ribosomal protein S21 / DNA-directed RNA polymerase subunit beta'
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsDemo, G. / Rasouly, A. / Vasilyev, N. / Loveland, A.B. / Diaz-Avalos, R. / Grigorieff, N. / Nudler, E. / Korostelev, A.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106105 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107465 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107329 United States
CitationJournal: Elife / Year: 2017
Title: Structure of RNA polymerase bound to ribosomal 30S subunit.
Authors: Gabriel Demo / Aviram Rasouly / Nikita Vasilyev / Vladimir Svetlov / Anna B Loveland / Ruben Diaz-Avalos / Nikolaus Grigorieff / Evgeny Nudler / Andrei A Korostelev /
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 ...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 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 2.0Oct 25, 2017Group: Database references / Polymer sequence / Category: citation / citation_author / entity_poly
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity_poly.type
Revision 2.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 2.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: 16S rRNA
01: DNA-directed RNA polymerase subunit alpha
02: DNA-directed RNA polymerase subunit alpha
03: DNA-directed RNA polymerase subunit beta
04: DNA-directed RNA polymerase subunit beta'
05: DNA-directed RNA polymerase subunit omega
B: 30S ribosomal protein S1
E: 30S ribosomal protein S2
F: 30S ribosomal protein S3
G: 30S ribosomal protein S4
H: 30S ribosomal protein S5
I: 30S ribosomal protein S6
J: 30S ribosomal protein S7
K: 30S ribosomal protein S8
L: 30S ribosomal protein S9
M: 30S ribosomal protein S10
N: 30S ribosomal protein S11
O: 30S ribosomal protein S12
P: 30S ribosomal protein S13
Q: 30S ribosomal protein S14
R: 30S ribosomal protein S15
S: 30S ribosomal protein S16
T: 30S ribosomal protein S17
U: 30S ribosomal protein S18
V: 30S ribosomal protein S19
W: 30S ribosomal protein S20
X: 30S ribosomal protein S21


Theoretical massNumber of molelcules
Total (without water)1,141,70027
Polymers1,141,70027
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 16S rRNA


Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules 0102030405

#2: Protein DNA-directed RNA polymerase subunit alpha / Polymerase / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 25339.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, Z4665, ECs4160 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z6, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150560.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoB, ECS88_4448 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MIX3, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit beta' / Polymerase / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 151537.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, Z5561, ECs4911 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T8, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase subunit omega / Polymerase / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 8649.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, ECS88_4064 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MFL0, DNA-directed RNA polymerase

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30S ribosomal protein ... , 21 types, 21 molecules BEFGHIJKLMNOPQRSTUVWX

#6: Protein 30S ribosomal protein S1 /


Mass: 13310.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#7: Protein 30S ribosomal protein S2 /


Mass: 24253.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MBF0
#8: Protein 30S ribosomal protein S3 /


Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCS9
#9: Protein 30S ribosomal protein S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCR2
#10: Protein 30S ribosomal protein S5 /


Mass: 16532.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W3
#11: Protein 30S ribosomal protein S6 /


Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7NGD4
#12: Protein 30S ribosomal protein S7 /


Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCV6
#13: Protein 30S ribosomal protein S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCS1
#14: Protein 30S ribosomal protein S9 /


Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MBZ1
#15: Protein 30S ribosomal protein S10 /


Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCT6
#16: Protein 30S ribosomal protein S11 /


Mass: 12388.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCR3
#17: Protein 30S ribosomal protein S12 /


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCV7
#18: Protein 30S ribosomal protein S13 /


Mass: 12625.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T1
#19: Protein 30S ribosomal protein S14 /


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCS2
#20: Protein 30S ribosomal protein S15 /


Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MB86
#21: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MIU7
#22: Protein 30S ribosomal protein S17 /


Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCS6
#23: Protein 30S ribosomal protein S18 /


Mass: 7606.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MLK7
#24: Protein 30S ribosomal protein S19 /


Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCT1
#25: Protein 30S ribosomal protein S20 /


Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MAE3
#26: Protein 30S ribosomal protein S21 /


Mass: 7763.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A8A4M2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
130S ribosomal subunit and RNA polymerase complexCOMPLEX#1-#260MULTIPLE SOURCES
230S ribosomal subunitProkaryotic small ribosomal subunitCOMPLEX#1, #6-#261NATURAL
3RNA polymeraseCOMPLEX#2-#51RECOMBINANT
Molecular weightValue: 1.3 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
Details: 20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 50 nM 30S, 150 nM RNAP
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K
Details: 2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 25000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2527
Details: The average electron dose 40.0 (e-/A2) represents the total dose for one collected movie.
Image scansMovie frames/image: 50 / Used frames/image: 1-50

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Processing

EM software
IDNameVersionCategory
1cisTEM1particle selection
2SerialEM3.6image acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9FREALIGN9.11initial Euler assignment
10FREALIGN9.11final Euler assignment
11FREALIGN9.11classification
12FREALIGN9.113D reconstruction
13RSRefmodel refinement
14PHENIX1.11model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 184530
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15012 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 500 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient

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