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Yorodumi- EMDB-20090: CryoEM structure of SigmaS-transcription initiation complex with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20090 | |||||||||
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Title | CryoEM structure of SigmaS-transcription initiation complex with activator Crl | |||||||||
Map data | E.coli RNA polymerase transcription initiation complex | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of cellulose biosynthetic process / DNA-templated transcription initiation => GO:0006352 / 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 ...positive regulation of cellulose biosynthetic process / DNA-templated transcription initiation => GO:0006352 / 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 / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.26 Å | |||||||||
Authors | Jaramillo Cartagena A / Darst SA / Campbell EA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Structural basis for transcription activation by Crl through tethering of σ and RNA polymerase. Authors: Alexis Jaramillo Cartagena / Amy B Banta / Nikhil Sathyan / Wilma Ross / Richard L Gourse / Elizabeth A Campbell / Seth A Darst / Abstract: In bacteria, a primary σ-factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative σ-factors are used to coordinate expression of additional ...In bacteria, a primary σ-factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative σ-factors are used to coordinate expression of additional regulons in response to environmental conditions. Many alternative σ-factors are negatively regulated by anti-σ-factors. In , , and many other γ-proteobacteria, the transcription factor Crl positively regulates the alternative σ-regulon by promoting the association of σ with RNAP without interacting with promoter DNA. The molecular mechanism for Crl activity is unknown. Here, we determined a single-particle cryo-electron microscopy structure of Crl-σ-RNAP in an open promoter complex with a σ-regulon promoter. In addition to previously predicted interactions between Crl and domain 2 of σ (σ), the structure, along with -benzoylphenylalanine cross-linking, reveals that Crl interacts with a structural element of the RNAP β'-subunit that we call the β'-clamp-toe (β'CT). Deletion of the β'CT decreases activation by Crl without affecting basal transcription, highlighting the functional importance of the Crl-β'CT interaction. We conclude that Crl activates σ-dependent transcription in part through stabilizing σ-RNAP by tethering σ and the β'CT. We propose that Crl, and other transcription activators that may use similar mechanisms, be designated σ-activators. | |||||||||
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_20090.map.gz | 59.2 MB | EMDB map data format | |
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Header (meta data) | emd-20090-v30.xml emd-20090.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
Images | emd_20090.png | 78.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20090 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20090 | HTTPS FTP |
-Validation report
Summary document | emd_20090_validation.pdf.gz | 354 KB | Display | EMDB validaton report |
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Full document | emd_20090_full_validation.pdf.gz | 353.6 KB | Display | |
Data in XML | emd_20090_validation.xml.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20090 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20090 | HTTPS FTP |
-Related structure data
Related structure data | 6omfMC 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_20090.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E.coli RNA polymerase transcription initiation complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 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 : CryoEM structure of SigmaS-transcription initiation complex with ...
Entire | Name: CryoEM structure of SigmaS-transcription initiation complex with activator Crl |
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Components |
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-Supramolecule #1: CryoEM structure of SigmaS-transcription initiation complex with ...
Supramolecule | Name: CryoEM structure of SigmaS-transcription initiation complex with activator Crl type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 523.783 KDa |
-Macromolecule #1: Crl
Macromolecule | Name: Crl / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPHMTLPSGH PKSRLIKKFT ALGPYIREGQ CEDNRFFFDC LAVCVNVKPA PEKREFWGWW MELEAQEKRF TYRYQFGLFD KEGNWTVVPI NETEVVERLE YTLREFHEKL RDLLISMELA LEPSDDFNDE PVKLSA |
-Macromolecule #2: DNA-directed RNA polymerase subunit sigma-S
Macromolecule | Name: DNA-directed RNA polymerase subunit sigma-S / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SMSQNTLKVH DLNEDAEFDE NGVEAFDEKA LSEEEPSDND LAEEELLSQG ATQRVLDATQ LYLGEIGYSP LLTAEEEVYF ARRALRGDVA SRRRMIESNL RLVVKIARRY GNRGLALLDL IEEGNLGLIR AVEKFDPERG FRFSTYATWW IRQTIERAIM NQTRTIRLPI ...String: SMSQNTLKVH DLNEDAEFDE NGVEAFDEKA LSEEEPSDND LAEEELLSQG ATQRVLDATQ LYLGEIGYSP LLTAEEEVYF ARRALRGDVA SRRRMIESNL RLVVKIARRY GNRGLALLDL IEEGNLGLIR AVEKFDPERG FRFSTYATWW IRQTIERAIM NQTRTIRLPI HIVKELNVYL RTARELSHKL DHEPSAEEIA EQLDKPVDDV SRMLRLNERI TSVDTPLGGD SEKALLDILA DEKENGPEDT TQDDDMKQSI VKWLFELNAK QREVLARRFG LLGYEAATLE DVGREIGLTR ERVRQIQVEG LRRLREILQT QGLNIEALFR E |
-Macromolecule #3: DNA-directed RNA polymerase subunit alpha
Macromolecule | Name: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLAV RVQGKDEVIL TLNKSGIGPV TAADITHDGD VEIVKPQHVI CHLTDENASI SMRIKVQRGR GYVPASTRIH SEEDERPIGR ...String: MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLAV RVQGKDEVIL TLNKSGIGPV TAADITHDGD VEIVKPQHVI CHLTDENASI SMRIKVQRGR GYVPASTRIH SEEDERPIGR LLVDACYSPV ERIAYNVEAA RVEQRTDLDK LVIEMETNGT IDPEEAIRRA ATILAEQLEA FVDLEVLFQ |
-Macromolecule #4: DNA-directed RNA polymerase subunit beta
Macromolecule | Name: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 |
-Macromolecule #5: DNA-directed RNA polymerase subunit beta'
Macromolecule | Name: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: VKDLLKFLKA QTKTEEFDAI KIALASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCGV EVTQTKVRRE RMGHIELASP TAHIWFLKSL PSRIGLLLDM PLRDIERVLY FESYVVIEGG MTNLERQQIL TEEQYLDALE ...String: VKDLLKFLKA QTKTEEFDAI KIALASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCGV EVTQTKVRRE RMGHIELASP TAHIWFLKSL PSRIGLLLDM PLRDIERVLY FESYVVIEGG MTNLERQQIL TEEQYLDALE EFGDEFDAKM GAEAIQALLK SMDLEQECEQ LREELNETNS ETKRKKLTKR IKLLEAFVQS GNKPEWMILT VLPVLPPDLR PLVPLDGGRF ATSDLNDLYR RVINRNNRLK RLLDLAAPDI IVRNEKRMLQ EAVDALLDNG RRGRAITGSN KRPLKSLADM IKGKQGRFRQ NLLGKRVDYS GRSVITVGPY LRLHQCGLPK KMALELFKPF IYGKLELRGL ATTIKAAKKM VEREEAVVWD ILDEVIREHP VLLNRAPTLH RLGIQAFEPV LIEGKAIQLH PLVCAAYNAD FDGDQMAVHV PLTLEAQLEA RALMMSTNNI LSPANGEPII VPSQDVVLGL YYMTRDCVNA KGEGMVLTGP KEAERLYRSG LASLHARVKV RITEYEKDAN GELVAKTSLK DTTVGRAILW MIVPKGLPYS IVNQALGKKA ISKMLNTCYR ILGLKPTVIF ADQIMYTGFA YAARSGASVG IDDMVIPEKK HEIISEAEAE VAEIQEQFQS GLVTAGERYN KVIDIWAAAN DRVSKAMMDN LQTETVINRD GQEEKQVSFN SIYMMADSGA RGSAAQIRQL AGMRGLMAKP DGSIIETPIT ANFREGLNVL QYFISTHGAR KGLADTALKT ANSGYLTRRL VDVAQDLVVT EDDCGTHEGI MMTPVIEGGD VKEPLRDRVL GRVTAEDVLK PGTADILVPR NTLLHEQWCD LLEENSVDAV KVRSVVSCDT DFGVCAHCYG RDLARGHIIN KGEAIGVIAA QSIGEPGTQL TMRTFHIGGA ASRAAAESSI QVKNKGSIKL SNVKSVVNSS GKLVITSRNT ELKLIDEFGR TKESYKVPYG AVLAKGDGEQ VAGGETVANW DPHTMPVITE VSGFVRFTDM IDGQTITRQT DELTGLSSLV VLDSAERTAG GKDLRPALKI VDAQGNDVLI PGTDMPAQYF LPGKAIVQLE DGVQISSGDT LARIPQESGG TKDITGGLPR VADLFEARRP KEPAILAEIS GIVSFGKETK GKRRLVITPV DGSDPYEEMI PKWRQLNVFE GERVERGDVI SDGPEAPHDI LRLRGVHAVT RYIVNEVQDV YRLQGVKIND KHIEVIVRQM LRKATIVNAG SSDFLEGEQV EYSRVKIANR ELEANGKVGA TYSRDLLGIT KASLATESFI SAASFQETTR VLTEAAVAGK RDELRGLKEN VIVGRLIPAG TGYAYHQDRM RRRAAGEAPA APQVTAEDAS ASLAELLNAG LGGSDNELE |
-Macromolecule #6: DNA-directed RNA polymerase subunit omega
Macromolecule | Name: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN NQILDVRERQ EQQEQEAAEL QAVTAIAEG RR |
-Macromolecule #7: Template DNA strand
Macromolecule | Name: Template DNA strand / type: dna / ID: 7 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Sequence | String: GCTATGTCCC AGTAATTAAC GAGTAATAGT ATAGCACCGG CTATGTGTTC CGCTATTCTG AATTCG |
-Macromolecule #8: Non-template DNA strand
Macromolecule | Name: Non-template DNA strand / type: dna / ID: 8 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Sequence | String: CGAATTCAGA ATAGCGGAAC ACATAGCCGG TGCTATACTT AATCTCGTTA ATTACTGGGA CATAGC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: C-flat-1.2/1.3 4C / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.42 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 22500 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6omf: |