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- EMDB-26439: Transcription antitermination complex: NusA-containing "engaged" ... -

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Basic information

Entry
Database: EMDB / ID: EMD-26439
TitleTranscription antitermination complex: NusA-containing "engaged" Qlambda-loading complex
Map data
Sample
  • Complex: Transcription antitermination complex: NusA-containing "engaged" Qlambda-loading complex
    • DNA: x 2 types
    • Protein or peptide: x 7 types
    • RNA: x 1 types
  • Ligand: x 2 types
KeywordsRNA polymerase / DNA Binding / transcription / Q-dependent antitermination / Q antitermination factor / GENE REGULATION / TRANSFERASE-DNA-RNA complex
Function / homology
Function and homology information


submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / translation elongation factor activity / nitrate assimilation / DNA-directed RNA polymerase complex ...submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / translation elongation factor activity / nitrate assimilation / DNA-directed RNA polymerase complex / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / DNA-templated transcription termination / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / protein dimerization activity / DNA-binding transcription factor activity / response to antibiotic / nucleotide binding / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Antitermination protein Q / Antitermination protein Q superfamily / Antitermination protein Q / Heat shock protein DnaJ, cysteine-rich domain superfamily / Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain ...Antitermination protein Q / Antitermination protein Q superfamily / Antitermination protein Q / Heat shock protein DnaJ, cysteine-rich domain superfamily / Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / 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 / DNA repair Rad51/transcription factor NusA, alpha-helical / Type-1 KH domain profile. / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / Helix-hairpin-helix domain / : / 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 / S1 domain profile. / 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 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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 Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / 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 / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Antitermination protein / Transcription termination/antitermination protein NusA / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia phage Lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsYin Z / Ebright RH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM041376 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel.
Authors: Zhou Yin / Jeremy G Bird / Jason T Kaelber / Bryce E Nickels / Richard H Ebright /
Abstract: Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP ...Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element to yield a Q-loading complex, and they translocate with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. In previous work, we showed that the Q protein of bacteriophage 21 (Q21) functions by forming a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of pause and termination RNA hairpins. Here, we report atomic structures of four states on the pathway of antitermination by the Q protein of bacteriophage λ (Qλ), a Q protein that shows no sequence similarity to Q21 and that, unlike Q21, requires the transcription elongation factor NusA for efficient antipausing and antitermination. We report structures of Qλ, the Qλ-QBE complex, the NusA-free pre-engaged Qλ-loading complex, and the NusA-containing engaged Qλ-loading complex. The results show that Qλ, like Q21, forms a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of RNA hairpins. However, the results show that Qλ has no three-dimensional structural similarity to Q21, employs a different mechanism of QBE recognition than Q21, and employs a more complex process for loading onto RNAP than Q21, involving recruitment of Qλ to form a pre-engaged loading complex, followed by NusA-facilitated refolding of Qλ to form an engaged loading complex. The results establish that Qλ and Q21 are not structural homologs and are solely functional analogs.
History
DepositionMar 15, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26439.png

Downloads & links

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Map

FileDownload / File: emd_26439.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 256 pix.
= 262.144 Å		1.02 Å/pix.
x 256 pix.
= 262.144 Å		1.02 Å/pix.
x 256 pix.
= 262.144 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.024 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0402
Minimum - Maximum-0.11383765 - 0.22588174
Average (Standard dev.)0.000452148 (±0.008473982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 262.144 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_26439_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_26439_half_map_2.map
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Sample components

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Entire : Transcription antitermination complex: NusA-containing "engaged" ...

EntireName: Transcription antitermination complex: NusA-containing "engaged" Qlambda-loading complex
Components
  • Complex: Transcription antitermination complex: NusA-containing "engaged" Qlambda-loading complex
    • DNA: DNA (53-MER)
    • DNA: DNA (52-MER)
    • 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
    • Protein or peptide: Transcription termination/antitermination protein NusA
    • Protein or peptide: Antitermination protein
    • RNA: RNA (5'-R(*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Transcription antitermination complex: NusA-containing "engaged" ...

SupramoleculeName: Transcription antitermination complex: NusA-containing "engaged" Qlambda-loading complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 550 KDa

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Macromolecule #1: DNA (53-MER)

MacromoleculeName: DNA (53-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 18.933164 KDa
SequenceString: (DC)(DT)(DT)(DA)(DT)(DT)(DG)(DA)(DA)(DT) (DA)(DA)(DA)(DA)(DT)(DT)(DG)(DG)(DG)(DT) (DA)(DA)(DA)(DT)(DT)(DT)(DG)(DA)(DC) (DA)(DC)(DT)(DA)(DT)(DA)(DA)(DT)(DG)(DG) (DG) (DT)(DT)(DA)(DA)(DT)(DT) ...String:
(DC)(DT)(DT)(DA)(DT)(DT)(DG)(DA)(DA)(DT) (DA)(DA)(DA)(DA)(DT)(DT)(DG)(DG)(DG)(DT) (DA)(DA)(DA)(DT)(DT)(DT)(DG)(DA)(DC) (DA)(DC)(DT)(DA)(DT)(DA)(DA)(DT)(DG)(DG) (DG) (DT)(DT)(DA)(DA)(DT)(DT)(DC)(DG) (DC)(DT)(DC)(DG)(DT)(DT)(DG)(DT)(DG)(DG) (DT)(DA) (DG)

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Macromolecule #2: DNA (52-MER)

MacromoleculeName: DNA (52-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 18.600982 KDa
SequenceString: (DC)(DT)(DA)(DC)(DC)(DA)(DC)(DA)(DA)(DC) (DG)(DA)(DG)(DT)(DT)(DA)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DG)(DT)(DC)(DA)(DT)(DA) (DA)(DG)(DT)(DG)(DT)(DC)(DA)(DA)(DA)(DT) (DT) (DT)(DA)(DC)(DC)(DC)(DA) ...String:
(DC)(DT)(DA)(DC)(DC)(DA)(DC)(DA)(DA)(DC) (DG)(DA)(DG)(DT)(DT)(DA)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DG)(DT)(DC)(DA)(DT)(DA) (DA)(DG)(DT)(DG)(DT)(DC)(DA)(DA)(DA)(DT) (DT) (DT)(DA)(DC)(DC)(DC)(DA)(DA)(DT) (DT)(DT)(DT)(DA)(DT)(DT)(DC)(DA)(DA)(DT) (DA)(DA) (DG)

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Macromolecule #3: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 3 / 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 (E. coli)
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 #4: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / 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: 150.820875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #5: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 158.314891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 SDNELERRAS ENLYFQGHHH HHHHHHH

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #6: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 6 / 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 (E. coli)
SequenceString:
MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN NQILDVRERQ EQQEQEAAEL QAVTAIAEG RR

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #7: RNA polymerase sigma factor RpoD

MacromoleculeName: RNA polymerase sigma factor RpoD / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 71.912906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGHMEQNPQ SQLKLLVTRG KEQGYLTYAE VNDHLPEDIV DSDQIEDIIQ MINDMGIQVM EEAPDADDLM LAENTADED AAEAAAQVLS SVESEIGRTT DPVRMYMREM GTVELLTREG EIDIAKRIED GINQVQCSVA EYPEAITYLL E QYDRVEAE ...String:
MGSSHHHHHH SSGHMEQNPQ SQLKLLVTRG KEQGYLTYAE VNDHLPEDIV DSDQIEDIIQ MINDMGIQVM EEAPDADDLM LAENTADED AAEAAAQVLS SVESEIGRTT DPVRMYMREM GTVELLTREG EIDIAKRIED GINQVQCSVA EYPEAITYLL E QYDRVEAE EARLSDLITG FVDPNAEEDL APTATHVGSE LSQEDLDDDE DEDEEDGDDD SADDDNSIDP ELAREKFAEL RA QYVVTRD TIKAKGRSHA TAQEEILKLS EVFKQFRLVP KQFDYLVNSM RVMMDRVRTQ ERLIMKLCVE QCKMPKKNFI TLF TGNETS DTWFNAAIAM NKPWSEKLHD VSEEVHRALQ KLQQIEEETG LTIEQVKDIN RRMSIGEAKA RRAKKEMVEA NLRL VISIA KKYTNRGLQF LDLIQEGNIG LMKAVDKFEY RRGYKFSTYA TWWIRQAITR SIADQARTIR IPVHMIETIN KLNRI SRQM LQEMGREPTP EELAERMLMP EDKIRKVLKI AKEPISMETP IGDDEDSHLG DFIEDTTLEL PLDSATTESL RAATHD VLA GLTAREAKVL RMRFGIDMNT DYTLEEVGKQ FDVTRERIRQ IEAKALRKLR HPSRSEVLRS FLDD

UniProtKB: RNA polymerase sigma factor RpoD

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Macromolecule #8: Transcription termination/antitermination protein NusA

MacromoleculeName: Transcription termination/antitermination protein NusA
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 57.104047 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MNKEILAVVE AVSNEKALPR EKIFEALESA LATATKKKYE QEIDVRVQID RKSGDFDTFR RWLVVDEVT QPTKEITLEA ARYEDESLNL GDYVEDQIES VTFDRITTQT AKQVIVQKVR EAERAMVVDQ FREHEGEIIT G VVKKVNRD ...String:
MGSSHHHHHH SSGLVPRGSH MNKEILAVVE AVSNEKALPR EKIFEALESA LATATKKKYE QEIDVRVQID RKSGDFDTFR RWLVVDEVT QPTKEITLEA ARYEDESLNL GDYVEDQIES VTFDRITTQT AKQVIVQKVR EAERAMVVDQ FREHEGEIIT G VVKKVNRD NISLDLGNNA EAVILREDML PRENFRPGDR VRGVLYSVRP EARGAQLFVT RSKPEMLIEL FRIEVPEIGE EV IEIKAAA RDPGSRAKIA VKTNDKRIDP VGACVGMRGA RVQAVSTELG GERIDIVLWD DNPAQFVINA MAPADVASIV VDE DKHTMD IAVEAGNLAQ AIGRNGQNVR LASQLSGWEL NVMTVDDLQA KHQAEAHAAI DTFTKYLDID EDFATVLVEE GFST LEELA YVPMKELLEI EGLDEPTVEA LRERAKNALA TIAQAQEESL GDNKPADDLL NLEGVDRDLA FKLAARGVCT LEDLA EQGI DDLADIEGLT DEKAGALIMA ARNICWFGDE A

UniProtKB: Transcription termination/antitermination protein NusA

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Macromolecule #9: Antitermination protein

MacromoleculeName: Antitermination protein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 22.505967 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLESVAKFH SPKSPMMSDS PRATASDSLS GTDVMAAMGM AQSQAGFGMA AFCGKHELSQ NDKQKAINYL MQFAHKVSGK YRGVAKLEG NTKAKVLQVL ATFAYADYCR SAATPGARCR DCHGTGRAVD IAKTELWGRV VEKECGRCKG VGYSRMPASA A YRAVTMLI ...String:
MRLESVAKFH SPKSPMMSDS PRATASDSLS GTDVMAAMGM AQSQAGFGMA AFCGKHELSQ NDKQKAINYL MQFAHKVSGK YRGVAKLEG NTKAKVLQVL ATFAYADYCR SAATPGARCR DCHGTGRAVD IAKTELWGRV VEKECGRCKG VGYSRMPASA A YRAVTMLI PNLTQPTWSR TVKPLYDALV VQCHKEESIA DNILNAVTR

UniProtKB: Antitermination protein

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Macromolecule #10: RNA (5'-R(*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')

MacromoleculeName: RNA (5'-R(*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') / type: rna / ID: 10 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 3.626226 KDa
SequenceString:
UGGGAGAGGU A

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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

Concentration9 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
10.0 mMTris
100.0 mMsodium chlorideNaCl
1.0 mMmagnesium chlorideMgCl2
1.0 mMDTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 292 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1643 / Average exposure time: 5.0 sec. / Average electron dose: 1.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 511891
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6alf

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 12391
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 5 / Avg.num./class: 10000 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5lm7

source_name: PDB, initial_model_type: experimental model

5lm9

source_name: PDB, initial_model_type: experimental model

1lb2

source_name: PDB, initial_model_type: experimental model

4yln

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 100 / Target criteria: Correlation coefficient
Output model

PDB-7ubn:
Transcription antitermination complex: NusA-containing "engaged" Qlambda-loading complex

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