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- EMDB-12157: Structures of class I bacterial transcription complexes -

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Basic information

Entry
Database: EMDB / ID: EMD-12157
TitleStructures of class I bacterial transcription complexes
Map datalocal resolution map
Sample
  • Complex: Class I transcription complex
    • Complex: DNA-directed RNA polymerase
      • 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
      • Protein or peptide: RNA polymerase sigma factor RpoD
      • DNA: Class I pacrA promoter non-template DNA
      • DNA: Class I pacrA promoter template DNA
      • Protein or peptide: Transcriptional activator RamA
    • Complex: Class I transcription complex
Keywordsantibiotic resistance / bacterial transcription activator / cryoEM / 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 / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...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 / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / DNA-directed RNA polymerase complex / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / transcription antitermination / 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 / sequence-specific DNA binding / protein dimerization activity / DNA-binding transcription factor activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region ...: / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / 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 Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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, 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 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. / Homeobox-like domain superfamily / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / RNA polymerase sigma factor RpoD / Transcriptional activator RamA
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Klebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsYe FZ / Hao M
Funding support China, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N007816/1 China
Medical Research Council (MRC, United Kingdom)MR/P007503/1 China
National Science Foundation (NSF, China)81991531 China
CitationJournal: Adv Sci (Weinh) / Year: 2022
Title: Structures of Class I and Class II Transcription Complexes Reveal the Molecular Basis of RamA-Dependent Transcription Activation.
Authors: Min Hao / Fuzhou Ye / Milija Jovanovic / Ioly Kotta-Loizou / Qingqing Xu / Xiaohua Qin / Martin Buck / Xiaodong Zhang / Minggui Wang /
Abstract: Transcription activator RamA is linked to multidrug resistance of Klebsiella pneumoniae through controlling genes that encode efflux pumps (acrA) and porin-regulating antisense RNA (micF). In ...Transcription activator RamA is linked to multidrug resistance of Klebsiella pneumoniae through controlling genes that encode efflux pumps (acrA) and porin-regulating antisense RNA (micF). In bacteria, σ , together with activators, controls the majority of genes by recruiting RNA polymerase (RNAP) to the promoter regions. RNAP and σ form a holoenzyme that recognizes -35 and -10 promoter DNA consensus sites. Many activators bind upstream from the holoenzyme and can be broadly divided into two classes. RamA acts as a class I activator on acrA and class II activator on micF, respectively. The authors present biochemical and structural data on RamA in complex with RNAP-σ at the two promoters and the data reveal the molecular basis for how RamA assembles and interacts with core RNAP and activates transcription that contributes to antibiotic resistance. Further, comparing with CAP/TAP complexes reveals common and activator-specific features in activator binding and uncovers distinct roles of the two C-terminal domains of RNAP α subunit.
History
DepositionDec 23, 2020-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-7beg
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12157.png

Downloads & links

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Map

FileDownload / File: emd_12157.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 368 pix.
= 399.28 Å		1.09 Å/pix.
x 368 pix.
= 399.28 Å		1.09 Å/pix.
x 368 pix.
= 399.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.085 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.094454914 - 0.21741343
Average (Standard dev.)-0.000024551542 (±0.0058762426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 399.28003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0851.0851.085
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z399.280399.280399.280
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0940.217-0.000

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Supplemental data

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Sample components

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Entire : Class I transcription complex

EntireName: Class I transcription complex
Components
  • Complex: Class I transcription complex
    • Complex: DNA-directed RNA polymerase
      • 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
      • Protein or peptide: RNA polymerase sigma factor RpoD
      • DNA: Class I pacrA promoter non-template DNA
      • DNA: Class I pacrA promoter template DNA
      • Protein or peptide: Transcriptional activator RamA
    • Complex: Class I transcription complex

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Supramolecule #1: Class I transcription complex

SupramoleculeName: Class I transcription complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 600 KDa

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Supramolecule #2: DNA-directed RNA polymerase

SupramoleculeName: DNA-directed RNA polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#8
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Class I transcription complex

SupramoleculeName: Class I transcription complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#8
Source (natural)Organism: Klebsiella pneumoniae (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 (E. coli)
Molecular weightTheoretical: 36.55868 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (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 EAFVDLRDVR QP EVKEEKP EFDPILLRPV DDLELTVRSA NCLKAEAIHY IGDLVQRTEV ELLKTPNLGK KSLTEIKDVL ASRGLSLGMR LEN WPPASI ADE

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 (E. coli)
Molecular weightTheoretical: 150.820875 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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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 (E. coli)
Molecular weightTheoretical: 155.366781 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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'

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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 (E. coli)
Molecular weightTheoretical: 10.249547 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (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: RNA polymerase sigma factor RpoD

MacromoleculeName: RNA polymerase sigma factor RpoD / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 72.3445 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAHHHHHHSS GLEVLFQMEQ NPQSQLKLLV TRGKEQGYLT YAEVNDHLPE DIVDSDQIED IIQMINDMGI QVMEEAPDAD DLMLAENTA DEDAAEAAAQ VLSSVESEIG RTTDPVRMYM REMGTVELLT REGEIDIAKR IEDGINQVQC SVAEYPEAIT Y LLEQYDRV ...String:
MAHHHHHHSS GLEVLFQMEQ NPQSQLKLLV TRGKEQGYLT YAEVNDHLPE DIVDSDQIED IIQMINDMGI QVMEEAPDAD DLMLAENTA DEDAAEAAAQ VLSSVESEIG RTTDPVRMYM REMGTVELLT REGEIDIAKR IEDGINQVQC SVAEYPEAIT Y LLEQYDRV EAEEARLSDL ITGFVDPNAE EDLAPTATHV GSELSQEDLD DDEDEDEEDG DDDSADDDNS IDPELAREKF AE LRAQYVV TRDTIKAKGR SHATAQEEIL KLSEVFKQFR LVPKQFDYLV NSMRVMMDRV RTQERLIMKL CVEQCKMPKK NFI TLFTGN ETSDTWFNAA IAMNKPWSEK LHDVSEEVHR ALQKLQQIEE ETGLTIEQVK DINRRMSIGE AKARRAKKEM VEAN LRLVI SIAKKYTNRG LQFLDLIQEG NIGLMKAVDK FEYRRGYKFS TYATWWIRQA ITRSIADQAR TIRIPVHMIE TINKL NRIS RQMLQEMGRE PTPEELAERM LMPEDKIRKV LKIAKEPISM ETPIGDDEDS HLGDFIEDTT LELPLDSATT ESLRAA THD VLAGLTAREA KVLRMRFGID MNTDYTLEEV GKQFDVTRER IRQIEAKALR KLRHPSRSEV LRSFLDD

UniProtKB: RNA polymerase sigma factor RpoD

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Macromolecule #8: Transcriptional activator RamA

MacromoleculeName: Transcriptional activator RamA / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 15.51052 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAHHHHHHSS GLEVLFQMTI SAQVIDTIVE WIDDNLHQPL RIDDIARHAG YSKWHLQRLF LQYKGESLGR YIRERKLLLA ARDLRDTDQ RVYDICLKYG FDSQQTFTRV FTRTFNQPPG AYRKENHSRA H

UniProtKB: Transcriptional activator RamA

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Macromolecule #6: Class I pacrA promoter non-template DNA

MacromoleculeName: Class I pacrA promoter non-template DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 29.090672 KDa
SequenceString: (DT)(DT)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DC) (DG)(DT)(DG)(DC)(DC)(DA)(DT)(DA)(DG)(DG) (DT)(DT)(DA)(DA)(DT)(DG)(DA)(DC)(DT) (DT)(DT)(DA)(DC)(DA)(DG)(DA)(DG)(DG)(DT) (DT) (DA)(DC)(DG)(DT)(DT)(DT) ...String:
(DT)(DT)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DC) (DG)(DT)(DG)(DC)(DC)(DA)(DT)(DA)(DG)(DG) (DT)(DT)(DA)(DA)(DT)(DG)(DA)(DC)(DT) (DT)(DT)(DA)(DC)(DA)(DG)(DA)(DG)(DG)(DT) (DT) (DA)(DC)(DG)(DT)(DT)(DT)(DA)(DC) (DA)(DT)(DA)(DC)(DA)(DT)(DT)(DT)(DG)(DT) (DG)(DA) (DA)(DT)(DG)(DT)(DA)(DT)(DG) (DT)(DA)(DC)(DC)(DA)(DT)(DG)(DA)(DA)(DC) (DG)(DT)(DA) (DC)(DC)(DA)(DT)(DA)(DA) (DT)(DA)(DG)(DA)(DA)(DA)(DG)(DA)

GENBANK: GENBANK: AP023264.1

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Macromolecule #7: Class I pacrA promoter template DNA

MacromoleculeName: Class I pacrA promoter template DNA / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 28.886588 KDa
SequenceString: (DT)(DC)(DT)(DT)(DT)(DC)(DT)(DA)(DT)(DT) (DA)(DT)(DG)(DG)(DT)(DC)(DA)(DT)(DG)(DC) (DT)(DA)(DT)(DG)(DG)(DT)(DA)(DC)(DA) (DT)(DA)(DC)(DA)(DT)(DT)(DC)(DA)(DC)(DA) (DA) (DA)(DT)(DG)(DT)(DA)(DT) ...String:
(DT)(DC)(DT)(DT)(DT)(DC)(DT)(DA)(DT)(DT) (DA)(DT)(DG)(DG)(DT)(DC)(DA)(DT)(DG)(DC) (DT)(DA)(DT)(DG)(DG)(DT)(DA)(DC)(DA) (DT)(DA)(DC)(DA)(DT)(DT)(DC)(DA)(DC)(DA) (DA) (DA)(DT)(DG)(DT)(DA)(DT)(DG)(DT) (DA)(DA)(DA)(DC)(DG)(DT)(DA)(DA)(DC)(DC) (DT)(DC) (DT)(DG)(DT)(DA)(DA)(DA)(DG) (DT)(DC)(DA)(DT)(DT)(DA)(DA)(DC)(DC)(DT) (DA)(DT)(DG) (DG)(DC)(DA)(DC)(DG)(DA) (DA)(DA)(DA)(DA)(DC)(DC)(DA)(DA)

GENBANK: GENBANK: CP052372.1

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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

Concentration0.5 mg/mL
BufferpH: 8 / Component:
ConcentrationFormula
20.0 mMTRIS
50.0 mMNaCl
/ Details: 20 mM Tris pH 8, 50 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 3472 / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1328947
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4ylp

Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39164
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 3

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Atomic model buiding 1

Initial modelPDB ID:

4ylp


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7beg:
Structures of class I bacterial transcription complexes

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