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- EMDB-76373: Pre-translocated RNA polymerase elemental paused elongation compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-76373
TitlePre-translocated RNA polymerase elemental paused elongation complex, TL open with ppGpp (ePEC open + ppGpp)
Map datafull/unsharpened map
Sample
  • Complex: Bacterial RNA polymerase elemental paused elongation complex
    • Complex: RNA polymerase
      • Protein or peptide: x 4 types
    • Complex: DNA and RNA
      • DNA: x 2 types
      • RNA: x 1 types
  • Ligand: x 5 types
Keywordselongation / pausing / pause escape / ppGpp / stringent response / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA complex
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMueller AU / Darst SA / Landick R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM038660 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118130 United States
CitationJournal: bioRxiv / Year: 2026
Title: ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition.
Authors: Andreas U Mueller / Rachel A Mooney / Michael D Engstrom / Yu Bao / Michael B Wolfe / Balendra Sah / Jonathan Buscher / Jason Saba / James Liu / Seth A Darst / Robert Landick /
Abstract: The signaling molecules guanosine 5'-tri/diphosphate 3'-diphosphate, (p)ppGpp, control bacterial protein synthesis rates and cell growth by targeting transcription, translation, NTP synthesis, and ...The signaling molecules guanosine 5'-tri/diphosphate 3'-diphosphate, (p)ppGpp, control bacterial protein synthesis rates and cell growth by targeting transcription, translation, NTP synthesis, and other functions. In lineages like , (p)ppGpp produced in response to charged-tRNA deficiency directly targets transcribing RNAP polymerase (RNAP) to match its pace to the pioneering ribosome on the nascent RNA (transcription-translation coupling). However, the mechanism by which (p)ppGpp slows RNAP is poorly defined. (p)ppGpp may allosterically stimulate RNAP pausing, inhibit catalysis, promote backtracking, compete for substrate GTP, inhibit GTP synthesis, or uncouple transcription-translation by inhibiting translation. Using a combination of cryo-EM, biochemical assays, and quantitative nascent elongating transcript sequencing (qNET-seq), we establish that (p)ppGpp allosterically regulates pausing and nucleotide addition via distinct motions of the RNAP swivel module and both competes with and lowers GTP in vivo. (p)ppGpp stimulates swiveling at pause sites to delay escape but may also inhibit counter-swiveling required in every round of nucleotide addition.
History
DepositionMar 30, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76373.png

Downloads & links

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Map

FileDownload / File: emd_76373.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull/unsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 413.184 Å		1.08 Å/pix.
x 384 pix.
= 413.184 Å		1.08 Å/pix.
x 384 pix.
= 413.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.7985986 - 2.0015876
Average (Standard dev.)0.0011448476 (±0.046653375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 413.184 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map (b-factor -76.4)

Fileemd_76373_additional_1.map
Annotationsharpened map (b-factor -76.4)
Projections & Slices
AxesZYX

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Histogram

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Additional map: locally filtered map

Fileemd_76373_additional_2.map
Annotationlocally filtered map
Projections & Slices
AxesZYX

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Histogram

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Additional map: local resolution map

Fileemd_76373_additional_3.map
Annotationlocal resolution map
Projections & Slices
AxesZYX

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Histogram

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Half map: half map A

Fileemd_76373_half_map_1.map
Annotationhalf map A
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_76373_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : Bacterial RNA polymerase elemental paused elongation complex

EntireName: Bacterial RNA polymerase elemental paused elongation complex
Components
  • Complex: Bacterial RNA polymerase elemental paused elongation complex
    • Complex: 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
    • Complex: DNA and RNA
      • DNA: DNA non-template strand
      • DNA: DNA template strand
      • RNA: RNA scaffold
  • Ligand: CHAPSO
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: GUANOSINE-5',3'-TETRAPHOSPHATE
  • Ligand: water

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Supramolecule #1: Bacterial RNA polymerase elemental paused elongation complex

SupramoleculeName: Bacterial RNA polymerase elemental paused elongation complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: Complexes were reconstituted on a DNA-RNA scaffold.
Molecular weightTheoretical: 440 KDa

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Supramolecule #2: RNA polymerase

SupramoleculeName: RNA polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: DNA and RNA

SupramoleculeName: DNA and RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2, #7
Source (natural)Organism: Escherichia coli (E. coli) / Synthetically produced: Yes

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Macromolecule #1: DNA non-template strand

MacromoleculeName: DNA non-template strand / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 19.159273 KDa
SequenceString: (DG)(DC)(DG)(DT)(DG)(DC)(DA)(DA)(DG)(DG) (DA)(DG)(DG)(DT)(DT)(DG)(DT)(DA)(DT)(DG) (DG)(DA)(DA)(DC)(DT)(DC)(DG)(DT)(DA) (DA)(DT)(DC)(DA)(DT)(DG)(DC)(DA)(DC)(DC) (DC) (DG)(DT)(DA)(DA)(DA)(DT) ...String:
(DG)(DC)(DG)(DT)(DG)(DC)(DA)(DA)(DG)(DG) (DA)(DG)(DG)(DT)(DT)(DG)(DT)(DA)(DT)(DG) (DG)(DA)(DA)(DC)(DT)(DC)(DG)(DT)(DA) (DA)(DT)(DC)(DA)(DT)(DG)(DC)(DA)(DC)(DC) (DC) (DG)(DT)(DA)(DA)(DA)(DT)(DT)(DC) (DA)(DC)(DC)(DG)(DG)(DT)(DT)(DC)(DA)(DG) (DA)(DC) (DC)(DG)

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Macromolecule #2: DNA template strand

MacromoleculeName: DNA template strand / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 19.030188 KDa
SequenceString: (DC)(DG)(DG)(DT)(DC)(DT)(DG)(DA)(DA)(DC) (DC)(DG)(DG)(DT)(DG)(DA)(DA)(DT)(DT)(DT) (DA)(DC)(DG)(DG)(DG)(DT)(DG)(DC)(DA) (DA)(DC)(DT)(DA)(DT)(DA)(DC)(DG)(DA)(DG) (DT) (DT)(DC)(DC)(DA)(DT)(DA) ...String:
(DC)(DG)(DG)(DT)(DC)(DT)(DG)(DA)(DA)(DC) (DC)(DG)(DG)(DT)(DG)(DA)(DA)(DT)(DT)(DT) (DA)(DC)(DG)(DG)(DG)(DT)(DG)(DC)(DA) (DA)(DC)(DT)(DA)(DT)(DA)(DC)(DG)(DA)(DG) (DT) (DT)(DC)(DC)(DA)(DT)(DA)(DC)(DA) (DA)(DC)(DC)(DT)(DC)(DC)(DT)(DT)(DG)(DC) (DA)(DC) (DG)(DC)

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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 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 #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 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 #5: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 5 / Details: C-terminal tag LELEVLFQGPSSGHHHHHHHHHH / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 158.105672 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 SDNELELEVL FQGPSSGHHH 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 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 #7: RNA scaffold

MacromoleculeName: RNA scaffold / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.944894 KDa
SequenceString:
GCGGUCUAGU CUUACCGCGA GGUAUAGUUG C

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Macromolecule #8: CHAPSO

MacromoleculeName: CHAPSO / type: ligand / ID: 8 / Number of copies: 1 / Formula: 1N7
Molecular weightTheoretical: 631.884 Da
Chemical component information

ChemComp-1N7:
CHAPSO / detergent*YM

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #11: GUANOSINE-5',3'-TETRAPHOSPHATE

MacromoleculeName: GUANOSINE-5',3'-TETRAPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: G4P
Molecular weightTheoretical: 603.16 Da
Chemical component information

ChemComp-G4P:
GUANOSINE-5',3'-TETRAPHOSPHATE

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Macromolecule #12: water

MacromoleculeName: water / type: ligand / ID: 12 / Number of copies: 180 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 8
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio generated map
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 104112
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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