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- EMDB-14190: CryoEM structure of bacterial transcription close complex (RPc) -
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Open data
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Basic information
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Title | CryoEM structure of bacterial transcription close complex (RPc) | |||||||||
![]() | Local filtered map: wild-type trancription close complex | |||||||||
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![]() | Cryo EM / RNA polymerase / transcription close complex / sigma54 / TRANSCRIPTION | |||||||||
Function / homology | ![]() DNA-binding transcription activator activity / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...DNA-binding transcription activator activity / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / DNA-directed RNA polymerase complex / nucleotidyltransferase activity / 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 / response to antibiotic / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Ye FZ / Zhang XD | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanisms of DNA opening revealed in AAA+ transcription complex structures. Authors: Fuzhou Ye / Forson Gao / Xiaojiao Liu / Martin Buck / Xiaodong Zhang / ![]() Abstract: Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter ...Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter complex, where DNA is opened up. In bacteria, RNAP relies on σ factors for its promoter specificities. Using a special form of sigma factor (σ), which forms a stable closed complex and requires its activator that belongs to the AAA+ ATPases (ATPases associated with diverse cellular activities), we obtained cryo-electron microscopy structures of transcription initiation complexes that reveal a previously unidentified process of DNA melting opening. The σ amino terminus threads through the locally opened up DNA and then becomes enclosed by the AAA+ hexameric ring in the activator-bound intermediate complex. Our structures suggest how ATP hydrolysis by the AAA+ activator could remove the σ inhibition while helping to open up DNA, using σ amino-terminal peptide as a pry bar. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 40 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.4 KB 23.4 KB | Display Display | ![]() |
Images | ![]() | 121.6 KB | ||
Filedesc metadata | ![]() | 9.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qwpMC ![]() 7qv9C ![]() 7qxiC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Local filtered map: wild-type trancription close complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with prom...
Entire | Name: Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex |
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Components |
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-Supramolecule #1: Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with prom...
Supramolecule | Name: Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 500 KDa |
-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: ![]() ![]() |
Molecular weight | Theoretical: 36.55868 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 EAFVDLRDVR QP EVKEEKP EFDPILLRPV DDLELTVRSA NCLKAEAIHY IGDLVQRTEV ELLKTPNLGK KSLTEIKDVL ASRGLSLGMR LEN WPPASI ADE 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: ![]() ![]() |
Molecular weight | Theoretical: 150.820875 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ SYSGNSELQY VSYRLGEPVF DVQECQIRG VTYSAPLRVK LRLVIYEREA PEGTVKDIKE QEVYMGEIPL MTDNGTFVIN GTERVIVSQL HRSPGVFFDS D KGKTHSSG ...String: MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ SYSGNSELQY VSYRLGEPVF DVQECQIRG VTYSAPLRVK LRLVIYEREA PEGTVKDIKE QEVYMGEIPL MTDNGTFVIN GTERVIVSQL HRSPGVFFDS D KGKTHSSG KVLYNARIIP YRGSWLDFEF DPKDNLFVRI DRRRKLPATI ILRALNYTTE QILDLFFEKV IFEIRDNKLQ ME LVPERLR GETASFDIEA NGKVYVEKGR RITARHIRQL EKDDVKLIEV PVEYIAGKVV AKDYIDESTG ELICAANMEL SLD LLAKLS QSGHKRIETL FTNDLDHGPY ISETLRVDPT NDRLSALVEI YRMMRPGEPP TREAAESLFE NLFFSEDRYD LSAV GRMKF NRSLLREEIE GSGILSKDDI IDVMKKLIDI RNGKGEVDDI DHLGNRRIRS VGEMAENQFR VGLVRVERAV KERLS LGDL DTLMPQDMIN AKPISAAVKE FFGSSQLSQF MDQNNPLSEI THKRRISALG PGGLTRERAG FEVRDVHPTH YGRVCP IET PEGPNIGLIN SLSVYAQTNE YGFLETPYRK VTDGVVTDEI HYLSAIEEGN YVIAQANSNL DEEGHFVEDL VTCRSKG ES SLFSRDQVDY MDVSTQQVVS VGASLIPFLE HDDANRALMG ANMQRQAVPT LRADKPLVGT GMERAVAVDS GVTAVAKR G GVVQYVDASR IVIKVNEDEM YPGEAGIDIY NLTKYTRSNQ NTCINQMPCV SLGEPVERGD VLADGPSTDL GELALGQNM RVAFMPWNGY NFEDSILVSE RVVQEDRFTT IHIQELACVS RDTKLGPEEI TADIPNVGEA ALSKLDESGI VYIGAEVTGG DILVGKVTP KGETQLTPEE KLLRAIFGEK ASDVKDSSLR VPNGVSGTVI DVQVFTRDGV EKDKRALEIE EMQLKQAKKD L SEELQILE AGLFSRIRAV LVAGGVEAEK LDKLPRDRWL ELGLTDEEKQ NQLEQLAEQY DELKHEFEKK LEAKRRKITQ GD DLAPGVL KIVKVYLAVK RRIQPGDKMA GRHGNKGVIS KINPIEDMPY DENGTPVDIV LNPLGVPSRM NIGQILETHL GMA AKGIGD KINAMLKQQQ EVAKLREFIQ RAYDLGADVR QKVDLSTFSD EEVMRLAENL RKGMPIATPV FDGAKEAEIK ELLK LGDLP TSGQIRLYDG RTGEQFERPV TVGYMYMLKL NHLVDDKMHA RSTGSYSLVT QQPLGGKAQF GGQRFGEMEV WALEA YGAA YTLQEMLTVK SDDVNGRTKM YKNIVDGNHQ MEPGMPESFN VLLKEIRSLG INIELEDE 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: ![]() ![]() |
Molecular weight | Theoretical: 155.366781 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKDLLKFLKA QTKTEEFDAI KIALASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCG VEVTQTKVRR ERMGHIELAS PTAHIWFLKS LPSRIGLLLD MPLRDIERVL YFESYVVIEG GMTNLERQQI L TEEQYLDA ...String: MKDLLKFLKA QTKTEEFDAI KIALASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCG VEVTQTKVRR ERMGHIELAS PTAHIWFLKS LPSRIGLLLD MPLRDIERVL YFESYVVIEG GMTNLERQQI L TEEQYLDA LEEFGDEFDA KMGAEAIQAL LKSMDLEQEC EQLREELNET NSETKRKKLT KRIKLLEAFV QSGNKPEWMI LT VLPVLPP DLRPLVPLDG GRFATSDLND LYRRVINRNN RLKRLLDLAA PDIIVRNEKR MLQEAVDALL DNGRRGRAIT GSN KRPLKS LADMIKGKQG RFRQNLLGKR VDYSGRSVIT VGPYLRLHQC GLPKKMALEL FKPFIYGKLE LRGLATTIKA AKKM VEREE AVVWDILDEV IREHPVLLNR APTLHRLGIQ AFEPVLIEGK AIQLHPLVCA AYNADFDGDQ MAVHVPLTLE AQLEA RALM MSTNNILSPA NGEPIIVPSQ DVVLGLYYMT RDCVNAKGEG MVLTGPKEAE RLYRSGLASL HARVKVRITE YEKDAN GEL VAKTSLKDTT VGRAILWMIV PKGLPYSIVN QALGKKAISK MLNTCYRILG LKPTVIFADQ IMYTGFAYAA RSGASVG ID DMVIPEKKHE IISEAEAEVA EIQEQFQSGL VTAGERYNKV IDIWAAANDR VSKAMMDNLQ TETVINRDGQ EEKQVSFN S IYMMADSGAR GSAAQIRQLA GMRGLMAKPD GSIIETPITA NFREGLNVLQ YFISTHGARK GLADTALKTA NSGYLTRRL VDVAQDLVVT EDDCGTHEGI MMTPVIEGGD VKEPLRDRVL GRVTAEDVLK PGTADILVPR NTLLHEQWCD LLEENSVDAV KVRSVVSCD TDFGVCAHCY GRDLARGHII NKGEAIGVIA AQSIGEPGTQ LTMRTFHIGG AASRAAAESS IQVKNKGSIK L SNVKSVVN SSGKLVITSR NTELKLIDEF GRTKESYKVP YGAVLAKGDG EQVAGGETVA NWDPHTMPVI TEVSGFVRFT DM IDGQTIT RQTDELTGLS SLVVLDSAER TAGGKDLRPA LKIVDAQGND VLIPGTDMPA QYFLPGKAIV QLEDGVQISS GDT LARIPQ ESGGTKDITG GLPRVADLFE ARRPKEPAIL AEISGIVSFG KETKGKRRLV ITPVDGSDPY EEMIPKWRQL NVFE GERVE RGDVISDGPE APHDILRLRG VHAVTRYIVN EVQDVYRLQG VKINDKHIEV IVRQMLRKAT IVNAGSSDFL EGEQV EYSR VKIANRELEA NGKVGATYSR DLLGITKASL ATESFISAAS FQETTRVLTE AAVAGKRDEL RGLKENVIVG RLIPAG TGY AYHQDRMRRR AAGEAPAAPQ VTAEDASASL AELLNAGLGG SDNE 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: ![]() ![]() |
Molecular weight | Theoretical: 10.249547 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN NQILDVRERQ EQQEQEAAEL QAVTAIAEG RR UniProtKB: DNA-directed RNA polymerase subunit omega |
-Macromolecule #5: RNA polymerase sigma-54 factor
Macromolecule | Name: RNA polymerase sigma-54 factor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 56.151 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MKQGLQLRLS QQLAMTPQLQ QAIRLLQLST LELQQELQQA LESNPLLEET DLHDEVEAKE VEDRESLDT VDALEQKEMP DELPLDASWD EIYTAGTPSG NGVDYQDDEL PVYQGETTQT LQDYLMWQVE LTPFTDTDRA I ATSIVDAV ...String: MGSSHHHHHH SSGLVPRGSH MKQGLQLRLS QQLAMTPQLQ QAIRLLQLST LELQQELQQA LESNPLLEET DLHDEVEAKE VEDRESLDT VDALEQKEMP DELPLDASWD EIYTAGTPSG NGVDYQDDEL PVYQGETTQT LQDYLMWQVE LTPFTDTDRA I ATSIVDAV DDTGYLTIQI EDIVDSIGDD EIGLEEVEAV LKRIQRFDPV GVAAKDLRDC LLIQLSQFAK ETPWLEEARL II SDHLDLL ANHDFRTLMR VTRLKEEVLK EAVNLIQSLD PRPGQSIQTS EPEYVIPDVL VRKVSGRWTV ELNADSIPRL KIN QQYAAM GNSARNDADG QFIRSNLQEA RWLIKSLESR NDTLLRVSRC IVEQQQAFFE QGEEYMKPMV LADIAQAVEM HEST ISRVT TQKYLHSPRG IFELKYFFSS HVNTEGGGEA SSTAIRALVK KLIAAENPAK PLSDSKLTSM LSEQGIMVAR RTVAK YRES LSIPPSNQRK QLV UniProtKB: RNA polymerase sigma-54 factor |
-Macromolecule #6: Non-Template promoter DNA
Macromolecule | Name: Non-Template promoter DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 19.439387 KDa |
Sequence | String: (DG)(DA)(DG)(DA)(DC)(DG)(DG)(DC)(DT)(DG) (DG)(DC)(DA)(DC)(DG)(DA)(DC)(DT)(DT)(DT) (DT)(DG)(DC)(DA)(DC)(DG)(DA)(DT)(DC) (DA)(DG)(DC)(DC)(DC)(DT)(DG)(DG)(DG)(DC) (DG) (DC)(DG)(DC)(DA)(DT)(DG) ...String: (DG)(DA)(DG)(DA)(DC)(DG)(DG)(DC)(DT)(DG) (DG)(DC)(DA)(DC)(DG)(DA)(DC)(DT)(DT)(DT) (DT)(DG)(DC)(DA)(DC)(DG)(DA)(DT)(DC) (DA)(DG)(DC)(DC)(DC)(DT)(DG)(DG)(DG)(DC) (DG) (DC)(DG)(DC)(DA)(DT)(DG)(DC)(DT) (DG)(DT)(DT)(DG)(DC)(DG)(DC)(DA)(DT)(DT) (DC)(DA) (DT)(DG)(DT) |
-Macromolecule #7: Template promoter DNA
Macromolecule | Name: Template promoter DNA / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 19.40441 KDa |
Sequence | String: (DA)(DC)(DA)(DT)(DG)(DA)(DA)(DT)(DG)(DC) (DG)(DC)(DA)(DA)(DC)(DA)(DG)(DC)(DA)(DT) (DG)(DC)(DG)(DC)(DG)(DC)(DC)(DC)(DA) (DG)(DG)(DG)(DC)(DT)(DG)(DA)(DT)(DC)(DG) (DT) (DG)(DC)(DA)(DA)(DA)(DA) ...String: (DA)(DC)(DA)(DT)(DG)(DA)(DA)(DT)(DG)(DC) (DG)(DC)(DA)(DA)(DC)(DA)(DG)(DC)(DA)(DT) (DG)(DC)(DG)(DC)(DG)(DC)(DC)(DC)(DA) (DG)(DG)(DG)(DC)(DT)(DG)(DA)(DT)(DC)(DG) (DT) (DG)(DC)(DA)(DA)(DA)(DA)(DG)(DT) (DC)(DG)(DT)(DG)(DC)(DC)(DA)(DG)(DC)(DC) (DG)(DT) (DC)(DT)(DC) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.5 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
Details: 20 mM Tris-HCl pH 8.0, 150 mM KCl, 10 mM MgCl2 | ||||||||||||
Grid | Model: Quantifoil / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | The sample was mxied in vitro in an order to form complex |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 14780 / Average exposure time: 4.1 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |