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- EMDB-21920: Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation ... -

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Basic information

Entry
Database: EMDB / ID: EMD-21920
TitleCryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex
Map dataBacillus subtilis RNAP Elongation Complex
Sample
  • Complex: DNA-directed RNA polymerase elongation complex
    • Complex: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', DNA-directed RNA polymerase subunit omega/DNA Complex
      • Protein or peptide: DNA-directed RNA polymerase subunit alpha
      • Protein or peptide: DNA-directed RNA polymerase subunit beta
      • Protein or peptide: DNA-directed RNA polymerase subunit beta'
      • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Complex: DNA, RNA
      • DNA: DNA (5'-D(*TP*GP*TP*CP*GP*GP*GP*CP*GP*TP*CP*CP*GP*CP*GP*CP*GP*CP*C)-3')
      • RNA: RNA (5'-R(P*GP*GP*CP*GP*CP*GP*CP*G)-3')
      • DNA: DNA (5'-D(P*AP*CP*GP*CP*CP*CP*GP*AP*CP*A)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsDNA-DEPENDENT RNA POLYMERASE / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA COMPLEX
Function / homology
Function and homology information


bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / response to antibiotic / DNA-templated transcription ...bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 ...DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesBacillus subtilis (bacteria) / Escherichia coli BL21(DE3) (bacteria) / Bacillus subtilis (strain 168) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsNewing T / Tolun G
CitationJournal: Nat Commun / Year: 2020
Title: Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD.
Authors: Timothy P Newing / Aaron J Oakley / Michael Miller / Catherine J Dawson / Simon H J Brown / James C Bouwer / Gökhan Tolun / Peter J Lewis /
Abstract: In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram- ...In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram-positive bacteria contain a transcription factor HelD that is able to remove and recycle stalled complexes, but it was not known how it performed this function. Here, using single particle cryo-electron microscopy, we have determined the structures of Bacillus subtilis RNA polymerase (RNAP) elongation and HelD complexes, enabling analysis of the conformational changes that occur in RNAP driven by HelD interaction. HelD has a 2-armed structure which penetrates deep into the primary and secondary channels of RNA polymerase. One arm removes nucleic acids from the active site, and the other induces a large conformational change in the primary channel leading to removal and recycling of the stalled polymerase, representing a novel mechanism for recycling transcription complexes in bacteria.
History
DepositionMay 6, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wvj
  • Surface level: 1.55
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21920.png

Downloads & links

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Map

FileDownload / File: emd_21920.map.gz / Format: CCP4 / Size: 20.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacillus subtilis RNAP Elongation Complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 188 pix.
= 157.92 Å		0.84 Å/pix.
x 172 pix.
= 144.48 Å		0.84 Å/pix.
x 166 pix.
= 139.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.55 / Movie #1: 1.55
Minimum - Maximum-5.7642713 - 10.3556385
Average (Standard dev.)-0.02620416 (±0.7741332)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin656155
Dimensions172166188
Spacing188172166
CellA: 157.92 Å / B: 144.48 Å / C: 139.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z188172166
origin x/y/z0.0000.0000.000
length x/y/z157.920144.480139.440
α/β/γ90.00090.00090.000
start NX/NY/NZ556561
NX/NY/NZ188172166
MAP C/R/S321
start NC/NR/NS616555
NC/NR/NS166172188
D min/max/mean-5.76410.356-0.026

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Supplemental data

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Sample components

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Entire : DNA-directed RNA polymerase elongation complex

EntireName: DNA-directed RNA polymerase elongation complex
Components
  • Complex: DNA-directed RNA polymerase elongation complex
    • Complex: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', DNA-directed RNA polymerase subunit omega/DNA Complex
      • Protein or peptide: DNA-directed RNA polymerase subunit alpha
      • Protein or peptide: DNA-directed RNA polymerase subunit beta
      • Protein or peptide: DNA-directed RNA polymerase subunit beta'
      • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Complex: DNA, RNA
      • DNA: DNA (5'-D(*TP*GP*TP*CP*GP*GP*GP*CP*GP*TP*CP*CP*GP*CP*GP*CP*GP*CP*C)-3')
      • RNA: RNA (5'-R(P*GP*GP*CP*GP*CP*GP*CP*G)-3')
      • DNA: DNA (5'-D(P*AP*CP*GP*CP*CP*CP*GP*AP*CP*A)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: DNA-directed RNA polymerase elongation complex

SupramoleculeName: DNA-directed RNA polymerase elongation complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Molecular weightTheoretical: 344.2 KDa

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Supramolecule #2: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polym...

SupramoleculeName: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', DNA-directed RNA polymerase subunit omega/DNA Complex
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Bacillus subtilis (bacteria)

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Supramolecule #3: DNA, RNA

SupramoleculeName: DNA, RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#7
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 34.842387 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIEIEKPKIE TVEISDDAKF GKFVVEPLER GYGTTLGNSL RRILLSSLPG AAVTSIQIDG VLHEFSTIEG VVEDVTTIIL HIKKLALKI YSDEEKTLEI DVQGEGTVTA ADITHDSDVE ILNPDLHIAT LGENASFRVR LTAQRGRGYT PADANKRDDQ P IGVIPIDS ...String:
MIEIEKPKIE TVEISDDAKF GKFVVEPLER GYGTTLGNSL RRILLSSLPG AAVTSIQIDG VLHEFSTIEG VVEDVTTIIL HIKKLALKI YSDEEKTLEI DVQGEGTVTA ADITHDSDVE ILNPDLHIAT LGENASFRVR LTAQRGRGYT PADANKRDDQ P IGVIPIDS IYTPVSRVSY QVENTRVGQV ANYDKLTLDV WTDGSTGPKE AIALGSKILT EHLNIFVGLT DEAQHAEIMV EK EEDQKEK VLEMTIEELD LSVRSYNCLK RAGINTVQEL ANKTEEDMMK VRNLGRKSLE EVKAKLEELG LGLRKDD

UniProtKB: DNA-directed RNA polymerase subunit alpha

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Macromolecule #2: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 133.847938 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTGQLVQYGR HRQRRSYARI SEVLELPNLI EIQTSSYQWF LDEGLREMFQ DISPIEDFTG NLSLEFIDYS LGEPKYPVEE SKERDVTYS APLRVKVRLI NKETGEVKDQ DVFMGDFPIM TDTGTFIING AERVIVSQLV RSPSVYFSGK VDKNGKKGFT A TVIPNRGA ...String:
MTGQLVQYGR HRQRRSYARI SEVLELPNLI EIQTSSYQWF LDEGLREMFQ DISPIEDFTG NLSLEFIDYS LGEPKYPVEE SKERDVTYS APLRVKVRLI NKETGEVKDQ DVFMGDFPIM TDTGTFIING AERVIVSQLV RSPSVYFSGK VDKNGKKGFT A TVIPNRGA WLEYETDAKD VVYVRIDRTR KLPVTVLLRA LGFGSDQEIL DLIGENEYLR NTLDKDNTEN SDKALLEIYE RL RPGEPPT VENAKSLLDS RFFDPKRYDL ANVGRYKINK KLHIKNRLFN QRLAETLVDP ETGEILAEKG QILDRRTLDK VLP YLENGI GFRKLYPNGG VVEDEVTLQS IKIFAPTDQE GEQVINVIGN AYIEEEIKNI TPADIISSIS YFFNLLHGVG DTDD IDHLG NRRLRSVGEL LQNQFRIGLS RMERVVRERM SIQDTNTITP QQLINIRPVI ASIKEFFGSS QLSQFMDQTN PLAEL THKR RLSALGPGGL TRERAGMEVR DVHYSHYGRM CPIETPEGPN IGLINSLSSY AKVNRFGFIE TPYRRVDPET GKVTGR IDY LTADEEDNYV VAQANARLDD EGAFIDDSIV ARFRGENTVV SRNRVDYMDV SPKQVVSAAT ACIPFLENDD SNRALMG AN MQRQAVPLMQ PEAPFVGTGM EYVSGKDSGA AVICKHPGIV ERVEAKNVWV RRYEEVDGQK VKGNLDKYSL LKFVRSNQ G TCYNQRPIVS VGDEVVKGEI LADGPSMELG ELALGRNVMV GFMTWDGYNY EDAIIMSERL VKDDVYTSIH IEEYESEAR DTKLGPEEIT RDIPNVGEDA LRNLDDRGII RIGAEVKDGD LLVGKVTPKG VTELTAEERL LHAIFGEKAR EVRDTSLRVP HGGGGIIHD VKVFNREDGD ELPPGVNQLV RVYIVQKRKI SEGDKMAGRH GNKGVISKIL PEEDMPYLPD GTPIDIMLNP L GVPSRMNI GQVLELHMGM AARYLGIHIA SPVFDGAREE DVWETLEEAG MSRDAKTVLY DGRTGEPFDN RVSVGIMYMI KL AHMVDDK LHARSTGPYS LVTQQPLGGK AQFGGQRFGE MEVWALEAYG AAYTLQEILT VKSDDVVGRV KTYEAIVKGD NVP EPGVPE SFKVLIKELQ SLGMDVKILS GDEEEIEMRD LEDEEDAKQA DGLALSGDEE PEETASADVE RDVVTKE

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #3: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 134.444953 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLDVNNFEYM NIGLASPDKI RSWSFGEVKK PETINYRTLK PEKDGLFCER IFGPTKDWEC HCGKYKRVRY KGVVCDRCGV EVTRAKVRR ERMGHIELAA PVSHIWYFKG IPSRMGLVLD MSPRALEEVI YFASYVVTDP ANTPLEKKQL LSEKEYRAYL D KYGNKFQA ...String:
MLDVNNFEYM NIGLASPDKI RSWSFGEVKK PETINYRTLK PEKDGLFCER IFGPTKDWEC HCGKYKRVRY KGVVCDRCGV EVTRAKVRR ERMGHIELAA PVSHIWYFKG IPSRMGLVLD MSPRALEEVI YFASYVVTDP ANTPLEKKQL LSEKEYRAYL D KYGNKFQA SMGAEAIHKL LQDIDLVKEV DMLKEELKTS QGQRRTRAIK RLEVLEAFRN SGNKPSWMIL DVLPVIPPEL RP MVQLDGG RFATSDLNDL YRRVINRNNR LKRLLDLGAP SIIVQNEKRM LQEAVDALID NGRRGRPVTG PGNRPLKSLS HML KGKQGR FRQNLLGKRV DYSGRSVIVV GPHLKMYQCG LPKEMALELF KPFVMKELVE KGLAHNIKSA KRKIERVQPE VWDV LESVI KEHPVLLNRA PTLHRLGIQA FEPTLVEGRA IRLHPLVCTA YNADFDGDQM AVHVPLSAEA QAEARILMLA AQNIL NPKD GKPVVTPSQD MVLGNYYLTL ERAGAVGEGM VFKNTDEALL AYQNGYVHLH TRVAVAANSL KNVTFTEEQR SKLLIT TVG KLVFNEILPE SFPYMNEPTK SNIEEKTPDR FFLEKGADVK AVIAQQPINA PFKKGILGKI IAEIFKRFHI TETSKML DR MKNLGFKYST KAGITVGVSD IVVLDDKQEI LEEAQSKVDN VMKQFRRGLI TEEERYERVI SIWSAAKDVI QGKLMKSL D ELNPIYMMSD SGARGNASNF TQLAGMRGLM ANPAGRIIEL PIKSSFREGL TVLEYFISTH GARKGLADTA LKTADSGYL TRRLVDVAQD VIIRETDCGT DRGILAKPLK EGTETIERLE ERLIGRFARK QVKHPETGEV LVNENELIDE DKALEIVEAG IEEVWIRSA FTCNTPHGVC KRCYGRNLAT GSDVEVGEAV GIIAAQSIGE PGTQLTMRTF HTGGVAGDDI TQGLPRIQEL F EARNPKGQ ATITEIDGTV VEINEVRDKQ QEIVVQGAVE TRSYTAPYNS RLKVAEGDKI TRGQVLTEGS IDPKELLKVT DL TTVQEYL LHEVQKVYRM QGVEIGDKHV EVMVRQMLRK VRVIDAGDTD VLPGTLLDIH QFTEANKKVL LEGNRPATGR PVL LGITKA SLETDSFLSA ASFQETTRVL TDAAIKGKRD ELLGLKENVI IGKLVPAGTG MMKYRKVKPV SNVQPTDDMV PVE

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #4: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 7.766921 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MLDPSIDSLM NKLDSKYTLV TVSARRAREM QIKKDQMIEH TISHKYVGKA LEEIDAGLLS FEKEDRE

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #5: DNA (5'-D(*TP*GP*TP*CP*GP*GP*GP*CP*GP*TP*CP*CP*GP*CP*GP*CP*GP*CP*...

MacromoleculeName: DNA (5'-D(*TP*GP*TP*CP*GP*GP*GP*CP*GP*TP*CP*CP*GP*CP*GP*CP*GP*CP*C)-3')
type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)
Molecular weightTheoretical: 5.814721 KDa
SequenceString:
(DT)(DG)(DT)(DC)(DG)(DG)(DG)(DC)(DG)(DT) (DC)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DC)

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Macromolecule #7: DNA (5'-D(P*AP*CP*GP*CP*CP*CP*GP*AP*CP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*CP*GP*CP*CP*CP*GP*AP*CP*A)-3') / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)
Molecular weightTheoretical: 2.998984 KDa
SequenceString:
(DA)(DC)(DG)(DC)(DC)(DC)(DG)(DA)(DC)(DA)

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Macromolecule #6: RNA (5'-R(P*GP*GP*CP*GP*CP*GP*CP*G)-3')

MacromoleculeName: RNA (5'-R(P*GP*GP*CP*GP*CP*GP*CP*G)-3') / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)
Molecular weightTheoretical: 2.596617 KDa
SequenceString:
GGCGCGCG

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.50 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMNH2C(CH2OH)3Tris
150.0 mMNaClSodium Chloride
10.0 mMMgCl2Magnesium Chloride
1.0 mM(HO2CCH2)2NCH2CH2N(CH2CO2H)2EDTA
5.0 mMHSCH2CH(OH)CH(OH)CH2SHDTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 32 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Details: Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Number real images: 5185 / Average exposure time: 9.0 sec. / Average electron dose: 52.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 59500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 463519
Startup modelType of model: INSILICO MODEL
In silico model: The initial model was generated using the "3D initial model" algorithm in RELION 3.1
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 58854
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6wvj:
Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex

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