+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23903 | |||||||||
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Title | Escherichia coli RNA polymerase and RapA binary complex | |||||||||
Map data | RNA polymerase and RapA binary complex | |||||||||
Sample |
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Keywords | RNAP recycling / RapA / Post-Termination Complex / PTC / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information ATP-dependent chromatin remodeler activity / 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 ...ATP-dependent chromatin remodeler activity / 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 / DNA-templated transcription initiation / transcription antitermination / cell motility / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / nucleic acid binding / protein dimerization activity / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Qayyum MZ / Murakami KS | |||||||||
Funding support | United States, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23903.map.gz | 166.6 MB | EMDB map data format | |
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Header (meta data) | emd-23903-v30.xml emd-23903.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
Images | emd_23903.png | 36 KB | ||
Filedesc metadata | emd-23903.cif.gz | 7.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23903 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23903 | HTTPS FTP |
-Validation report
Summary document | emd_23903_validation.pdf.gz | 624.2 KB | Display | EMDB validaton report |
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Full document | emd_23903_full_validation.pdf.gz | 623.8 KB | Display | |
Data in XML | emd_23903_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_23903_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23903 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23903 | HTTPS FTP |
-Related structure data
Related structure data | 7mkqMC 7mknC 7mkoC 7mkpC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23903.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RNA polymerase and RapA binary complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Escherichia coli RNA polymerase and RapA binary complex
Entire | Name: Escherichia coli RNA polymerase and RapA binary complex |
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Components |
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-Supramolecule #1: Escherichia coli RNA polymerase and RapA binary complex
Supramolecule | Name: Escherichia coli RNA polymerase and RapA binary complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K-12 |
-Macromolecule #1: DNA-directed RNA polymerase subunit alpha
Macromolecule | Name: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 26.21383 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: DNA-directed RNA polymerase subunit beta
Macromolecule | Name: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 150.590547 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: 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 |
-Macromolecule #3: DNA-directed RNA polymerase subunit beta'
Macromolecule | Name: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 150.865766 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: 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' |
-Macromolecule #4: DNA-directed RNA polymerase subunit omega
Macromolecule | Name: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 10.249547 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN NQILDVRERQ EQQEQEAAEL QAVTAIAEG RR UniProtKB: DNA-directed RNA polymerase subunit omega |
-Macromolecule #5: RNA polymerase-associated protein RapA
Macromolecule | Name: RNA polymerase-associated protein RapA / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 109.897906 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MPFTLGQRWI SDTESELGLG TVVAVDARTV TLLFPSTGEN RLYARSDSPV TRVMFNPGDT ITSHDGWQMQ VEEVKEENGL LTYIGTRLD TEESGVALRE VFLDSKLVFS KPQDRLFAGQ IDRMDRFALR YRARKYSSEQ FRMPYSGLRG QRTSLIPHQL N IAHDVGRR ...String: MPFTLGQRWI SDTESELGLG TVVAVDARTV TLLFPSTGEN RLYARSDSPV TRVMFNPGDT ITSHDGWQMQ VEEVKEENGL LTYIGTRLD TEESGVALRE VFLDSKLVFS KPQDRLFAGQ IDRMDRFALR YRARKYSSEQ FRMPYSGLRG QRTSLIPHQL N IAHDVGRR HAPRVLLADE VGLGKTIEAG MILHQQLLSG AAERVLIIVP ETLQHQWLVE MLRRFNLRFA LFDDERYAEA QH DAYNPFD TEQLVICSLD FARRSKQRLE HLCEAEWDLL VVDEAHHLVW SEDAPSREYQ AIEQLAEHVP GVLLLTATPE QLG MESHFA RLRLLDPNRF HDFAQFVEEQ KNYRPVADAV AMLLAGNKLS NDELNMLGEM IGEQDIEPLL QAANSDSEDA QSAR QELVS MLMDRHGTSR VLFRNTRNGV KGFPKRELHT IKLPLPTQYQ TAIKVSGIMG ARKSAEDRAR DMLYPERIYQ EFEGD NATW WNFDPRVEWL MGYLTSHRSQ KVLVICAKAA TALQLEQVLR EREGIRAAVF HEGMSIIERD RAAAWFAEED TGAQVL LCS EIGSEGRNFQ FASHMVMFDL PFNPDLLEQR IGRLDRIGQA HDIQIHVPYL EKTAQSVLVR WYHEGLDAFE HTCPTGR TI YDSVYNDLIN YLASPDQTEG FDDLIKNCRE QHEALKAQLE QGRDRLLEIH SNGGEKAQAL AESIEEQDDD TNLIAFAM N LFDIIGINQD DRGDNMIVLT PSDHMLVPDF PGLSEDGITI TFDREVALAR EDAQFITWEH PLIRNGLDLI LSGDTGSST ISLLKNKALP VGTLLVELIY VVEAQAPKQL QLNRFLPPTP VRMLLDKNGN NLAAQVEFET FNRQLNAVNR HTGSKLVNAV QQDVHAILQ LGEAQIEKSA RALIDAARNE ADEKLSAELS RLEALRAVNP NIRDDELTAI ESNRQQVMES LDQAGWRLDA L RLIVVTHQ UniProtKB: RNA polymerase-associated protein RapA |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88511 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING |