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- EMDB-23902: Escherichia coli RNA polymerase core enzyme -

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Basic information

Entry
Database: EMDB / ID: EMD-23902
TitleEscherichia coli RNA polymerase core enzyme
Map dataRNA polymerase core enzyme
Sample
  • Complex: Escherichia coli RNA polymerase core enzyme
    • 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
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsRNAP recycling / RapA / Post-Termination Complex / PTC / TRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex ...RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytosol
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, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/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, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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 alpha / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit omega
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsQayyum MZ / Murakami KS
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM087350 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM131860 United States
CitationJournal: J Biol Chem / Year: 2021
Title: Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli.
Authors: M Zuhaib Qayyum / Vadim Molodtsov / Andrew Renda / Katsuhiko S Murakami /
Abstract: After transcription termination, cellular RNA polymerases (RNAPs) are occasionally trapped on DNA, impounded in an undefined post-termination complex (PTC), limiting the free RNAP pool and ...After transcription termination, cellular RNA polymerases (RNAPs) are occasionally trapped on DNA, impounded in an undefined post-termination complex (PTC), limiting the free RNAP pool and subsequently leading to inefficient transcription. In Escherichia coli, a Swi2/Snf2 family of ATPase called RapA is known to be involved in countering such inefficiency through RNAP recycling; however, the precise mechanism of this recycling is unclear. To better understand its mechanism, here we determined the structures of two sets of E. coli RapA-RNAP complexes, along with the RNAP core enzyme and the elongation complex, using cryo-EM. These structures revealed the large conformational changes of RNAP and RapA upon their association that has been implicated in the hindrance of PTC formation. Our results along with DNA-binding assays reveal that although RapA binds RNAP away from the DNA-binding main channel, its binding can allosterically close the RNAP clamp, thereby preventing its nonspecific DNA binding and PTC formation. Taken together, we propose that RapA acts as a guardian of RNAP by which RapA prevents nonspecific DNA binding of RNAP without affecting the binding of promoter DNA recognition σ factor, thereby enhancing RNAP recycling.
History
DepositionApr 26, 2021-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
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: 0.23
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.23
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mkp
  • Surface level: 0.23
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23902.png

Downloads & links

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Map

FileDownload / File: emd_23902.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNA polymerase core enzyme
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 388.8 Å		1.08 Å/pix.
x 360 pix.
= 388.8 Å		1.08 Å/pix.
x 360 pix.
= 388.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23 / Movie #1: 0.23
Minimum - Maximum-0.41388988 - 1.2745261
Average (Standard dev.)-0.00091975345 (±0.03018353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 388.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z388.800388.800388.800
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.4141.275-0.001

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Supplemental data

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Sample components

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Entire : Escherichia coli RNA polymerase core enzyme

EntireName: Escherichia coli RNA polymerase core enzyme
Components
  • Complex: Escherichia coli RNA polymerase core enzyme
    • 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
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Escherichia coli RNA polymerase core enzyme

SupramoleculeName: Escherichia coli RNA polymerase core enzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli K-12 (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: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 26.21383 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLA VRVQGKDEVI LTLNKSGIGP VTAADITHDG DVEIVKPQHV ICHLTDENAS ISMRIKVQRG RGYVPASTRI H SEEDERPI ...String:
MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLA VRVQGKDEVI LTLNKSGIGP VTAADITHDG DVEIVKPQHV ICHLTDENAS ISMRIKVQRG RGYVPASTRI H SEEDERPI GRLLVDACYS PVERIAYNVE AARVEQRTDL DKLVIEMETN GTIDPEEAIR RAATILAEQL EAFVDLRDV

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: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 150.590547 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: YSYTEKKRIR KDFGKRPQVL DVPYLLSIQL DSFQKFIEQD PEGQYGLEAA FRSVFPIQSY SGNSELQYVS YRLGEPVFDV QECQIRGVT YSAPLRVKLR LVIYEREAPE GTVKDIKEQE VYMGEIPLMT DNGTFVINGT ERVIVSQLHR SPGVFFDSDK G KTHSSGKV ...String:
YSYTEKKRIR KDFGKRPQVL DVPYLLSIQL DSFQKFIEQD PEGQYGLEAA FRSVFPIQSY SGNSELQYVS YRLGEPVFDV QECQIRGVT YSAPLRVKLR LVIYEREAPE GTVKDIKEQE VYMGEIPLMT DNGTFVINGT ERVIVSQLHR SPGVFFDSDK G KTHSSGKV LYNARIIPYR GSWLDFEFDP KDNLFVRIDR RRKLPATIIL RALNYTTEQI LDLFFEKVIF EIRDNKLQME LV PERLRGE TASFDIEANG KVYVEKGRRI TARHIRQLEK DDVKLIEVPV EYIAGKVVAK DYIDESTGEL ICAANMELSL DLL AKLSQS GHKRIETLFT NDLDHGPYIS ETLRVDPTND RLSALVEIYR MMRPGEPPTR EAAESLFENL FFSEDRYDLS AVGR MKFNR SLLREEIEGS GILSKDDIID VMKKLIDIRN GKGEVDDIDH LGNRRIRSVG EMAENQFRVG LVRVERAVKE RLSLG DLDT LMPQDMINAK PISAAVKEFF GSSQLSQFMD QNNPLSEITH KRRISALGPG GLTRERAGFE VRDVHPTHYG RVCPIE TPE GPNIGLINSL SVYAQTNEYG FLETPYRKVT DGVVTDEIHY LSAIEEGNYV IAQANSNLDE EGHFVEDLVT CRSKGES SL FSRDQVDYMD VSTQQVVSVG ASLIPFLEHD DANRALMGAN MQRQAVPTLR ADKPLVGTGM ERAVAVDSGV TAVAKRGG V VQYVDASRIV IKVNEDEMYP GEAGIDIYNL TKYTRSNQNT CINQMPCVSL GEPVERGDVL ADGPSTDLGE LALGQNMRV AFMPWNGYNF EDSILVSERV VQEDRFTTIH IQELACVSRD TKLGPEEITA DIPNVGEAAL SKLDESGIVY IGAEVTGGDI LVGKVTPKG ETQLTPEEKL LRAIFGEKAS DVKDSSLRVP NGVSGTVIDV QVFTRDGVEK DKRALEIEEM QLKQAKKDLS E ELQILEAG LFSRIRAVLV AGGVEAEKLD KLPRDRWLEL GLTDEEKQNQ LEQLAEQYDE LKHEFEKKLE AKRRKITQGD DL APGVLKI VKVYLAVKRR IQPGDKMAGR HGNKGVISKI NPIEDMPYDE NGTPVDIVLN PLGVPSRMNI GQILETHLGM AAK GIGDKI NAMLKQQQEV AKLREFIQRA YDLGADVRQK VDLSTFSDEE VMRLAENLRK GMPIATPVFD GAKEAEIKEL LKLG DLPTS GQIRLYDGRT GEQFERPVTV GYMYMLKLNH LVDDKMHARS TGSYSLVTQQ PLGGKAQFGG QRFGEMEVWA LEAYG AAYT LQEMLTVKSD DVNGRTKMYK NIVDGNHQME PGMPESFNVL LKEIRSLGIN IELEDE

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: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 150.865766 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: TEEFDAIKIA LASPDMIRSW SFGEVKKPET INYRTFKPER DGLFCARIFG PVKDYECLCG KYKRLKHRGV ICEKCGVEVT QTKVRRERM GHIELASPTA HIWFLKSLPS RIGLLLDMPL RDIERVLYFE SYVVIEGGMT NLERQQILTE EQYLDALEEF G DEFDAKMG ...String:
TEEFDAIKIA LASPDMIRSW SFGEVKKPET INYRTFKPER DGLFCARIFG PVKDYECLCG KYKRLKHRGV ICEKCGVEVT QTKVRRERM GHIELASPTA HIWFLKSLPS RIGLLLDMPL RDIERVLYFE SYVVIEGGMT NLERQQILTE EQYLDALEEF G DEFDAKMG AEAIQALLKS MDLEQECEQL REELNETNSE TKRKKLTKRI KLLEAFVQSG NKPEWMILTV LPVLPPDLRP LV PLDGGRF ATSDLNDLYR RVINRNNRLK RLLDLAAPDI IVRNEKRMLQ EAVDALLDNG RRGRAITGSN KRPLKSLADM IKG KQGRFR QNLLGKRVDY SGRSVITVGP YLRLHQCGLP KKMALELFKP FIYGKLELRG LATTIKAAKK MVEREEAVVW DILD EVIRE HPVLLNRAPT LHRLGIQAFE PVLIEGKAIQ LHPLVCAAYN ADFDGDQMAV HVPLTLEAQL EARALMMSTN NILSP ANGE PIIVPSQDVV LGLYYMTRDC VNAKGEGMVL TGPKEAERLY RSGLASLHAR VKVRITEYEK DANGELVAKT SLKDTT VGR AILWMIVPKG LPYSIVNQAL GKKAISKMLN TCYRILGLKP TVIFADQIMY TGFAYAARSG ASVGIDDMVI PEKKHEI IS EAEAEVAEIQ EQFQSGLVTA GERYNKVIDI WAAANDRVSK AMMDNLQTET VINRDGQEEK QVSFNSIYMM ADSGARGS A AQIRQLAGMR GLMAKPDGSI IETPITANFR EGLNVLQYFI STHGARKGLA DTALKTANSG YLTRRLVDVA QDLVVTEDD CGTHEGIMMT PVIEGGDVKE PLRDRVLGRV TAEDVLKPGT ADILVPRNTL LHEQWCDLLE ENSVDAVKVR SVVSCDTDFG VCAHCYGRD LARGHIINKG EAIGVIAAQS IGEPGTQLTM RTFHIGGAAS RAAAESSIQV KNKGSIKLSN VKSVVNSSGK L VITSRNTE LKLIDEFGRT KESYKVPYGA VLAKGDGEQV AGGETVANWD PHTMPVITEV SGFVRFTDMI DGQTITRQTD EL TGLSSLV VLDSAERTAG GKDLRPALKI VDAQGNDVLI PGTDMPAQYF LPGKAIVQLE DGVQISSGDT LARIPQESGG TKD ITGGLP RVADLFEARR PKEPAILAEI SGIVSFGKET KGKRRLVITP VDGSDPYEEM IPKWRQLNVF EGERVERGDV ISDG PEAPH DILRLRGVHA VTRYIVNEVQ DVYRLQGVKI NDKHIEVIVR QMLRKATIVN AGSSDFLEGE QVEYSRVKIA NRELE ANGK VGATYSRDLL GITKASLATE SFISAASFQE TTRVLTEAAV AGKRDELRGL KENVIVGRLI PAGTGYAYHQ DRMRRR AAG

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: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 10.249547 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN NQILDVRERQ EQQEQEAAEL QAVTAIAEG RR

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 235617
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING

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