EMDB-51264: RNAP-TopoI complex on long-overhang scaffold - orientation 2

Basic information

Entry

Database: EMDB / ID: EMD-51264

• Title: RNAP-TopoI complex on long-overhang scaffold - orientation 2
• Map data: RNAP-TopoI complex on long-overhang scaffold orientation 2 - unsharpened map

Sample

• Complex: RNAP-TopoI complex on long-overhang scaffold
  • Complex: DNA-directed RNA polymerase elongation complex
    • 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
    • DNA: non-template DNA strand
    • RNA: RNA
    • DNA: template DNA strand
  • Complex: DNA topoisomerase 1
    • Protein or peptide: DNA topoisomerase 1
• Ligand: MAGNESIUM ION
• Ligand: ZINC ION

• Keywords: RNA polymerase / topoisomerase / DNA topology / TRANSCRIPTION

Function / homology

Function:

RNA topoisomerase activity / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / DNA topological change / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / chromosome / 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 / cytoplasm / cytosol

Domain/homology:

DNA topoisomerase I, zinc ribbon-like, bacterial-type / : / Topoisomerase I zinc-ribbon-like / Topoisomerase I, zinc finger / DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / 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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / 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 Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / 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

Component:

DNA topoisomerase 1 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta

• Biological species: Escherichia coli (E. coli) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 3.9 Å
• Authors: Vidmar V / Weixlbaumer A / Lamour V

Funding support

France, 2 items

Organization	Grant number	Country
Agence Nationale de la Recherche (ANR)	ANR-21-CE11-0040-01	France
Agence Nationale de la Recherche (ANR)	ANR-10-INBS-05	France

• Citation: Journal: To Be Published; Title: DNA topoisomerase I acts as supercoiling sensor for transcription elongation in E. coli; Authors: Vidmar V / Borde C / Bruno L / Takacs M / Batisse C / Saint-Andre C / Zhu C / Espeli O / Lamour V / Weixlbaumer A

History

Deposition	Aug 5, 2024	-
Header (metadata) release	Nov 5, 2025	-
Map release	Nov 5, 2025	-
Update	Nov 5, 2025	-
Current status	Nov 5, 2025	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_51264.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: RNAP-TopoI complex on long-overhang scaffold orientation 2 - unsharpened map
• Voxel size: X=Y=Z: 0.99871 Å

Density

Contour Level	By AUTHOR: 0.174
Minimum - Maximum	-0.32428783 - 0.86595166
Average (Standard dev.)	0.0032761118 (±0.043935195)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 310 310 310 Spacing 310 310 310
Cell	A=B=C: 309.59998 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_51264_msk_1.map

Mask #2

• File: emd_51264_msk_2.map

Additional map: RNAP-TopoI complex on long-overhang scaffold orientation 2 -...

• File: emd_51264_additional_1.map
• Annotation: RNAP-TopoI complex on long-overhang scaffold orientation 2 - sharpened map

Additional map: RNAP-TopoI complex on long-overhang scaffold orientation 2 -...

• File: emd_51264_additional_2.map
• Annotation: RNAP-TopoI complex on long-overhang scaffold orientation 2 - lowpassfiltered map 12 A

Half map: RNAP-TopoI complex on long-overhang scaffold orientation 2 -...

• File: emd_51264_half_map_1.map
• Annotation: RNAP-TopoI complex on long-overhang scaffold orientation 2 - halfmap A

Half map: RNAP-TopoI complex on long-overhang scaffold orientation 2 -...

• File: emd_51264_half_map_2.map
• Annotation: RNAP-TopoI complex on long-overhang scaffold orientation 2 - halfmap B

Sample components

Entire : RNAP-TopoI complex on long-overhang scaffold

• Entire: Name: RNAP-TopoI complex on long-overhang scaffold

Components

• Complex: RNAP-TopoI complex on long-overhang scaffold
  • Complex: DNA-directed RNA polymerase elongation complex
    • 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
    • DNA: non-template DNA strand
    • RNA: RNA
    • DNA: template DNA strand
  • Complex: DNA topoisomerase 1
    • Protein or peptide: DNA topoisomerase 1
• Ligand: MAGNESIUM ION
• Ligand: ZINC ION

Supramolecule #1: RNAP-TopoI complex on long-overhang scaffold

• Supramolecule: Name: RNAP-TopoI complex on long-overhang scaffold / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
• Molecular weight: Theoretical: 100 KDa

Supramolecule #2: DNA-directed RNA polymerase elongation complex

• Supramolecule: Name: DNA-directed RNA polymerase elongation complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4, #6-#8
• Source (natural): Organism: Escherichia coli (E. coli)

Supramolecule #3: DNA topoisomerase 1

• Supramolecule: Name: DNA topoisomerase 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
• Source (natural): Organism: Escherichia coli (E. coli)

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
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 36.55868 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

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
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 150.820875 KDa
• 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 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
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 156.338891 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

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 FQ

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
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 10.249547 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN NQILDVRERQ EQQEQEAAEL QAVTAIAEG RR

UniProtKB: DNA-directed RNA polymerase subunit omega

Macromolecule #5: DNA topoisomerase 1

• Macromolecule: Name: DNA topoisomerase 1 / type: protein_or_peptide / ID: 5 / Details: N-terminal TwinStrep tag / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA topoisomerase
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 100.659328 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

GPWSHPQFEK GGGSGGGSGG SAWSHPQFEK HMGKALVIVE SPAKAKTINK YLGSDYVVKS SVGHIRDLPT SGSAAKKSAD STSTKTAKK PKKDERGALV NRMGVDPWHN WEAHYEVLPG KEKVVSELKQ LAEKADHIYL ATDLDREGEA IAWHLREVIG G DDARYSRV VFNEITKNAI RQAFNKPGEL NIDRVNAQQA RRFMDRVVGY MVSPLLWKKI ARGLSAGRVQ SVAVRLVVER ER EIKAFVP EEFWEVDAST TTPSGEALAL QVTHQNDKPF RPVNKEQTQA AVSLLEKARY SVLEREDKPT TSKPGAPFIT STL QQAAST RLGFGVKKTM MMAQRLYEAG YITYMRTDST NLSQDAVNMV RGYISDNFGK KYLPESPNQY ASKENSQEAH EAIR PSDVN VMAESLKDME ADAQKLYQLI WRQFVACQMT PAKYDSTTLT VGAGDFRLKA RGRILRFDGW TKVMPALRKG DEDRI LPAV NKGDALTLVE LTPAQHFTKP PARFSEASLV KELEKRGIGR PSTYASIIST IQDRGYVRVE NRRFYAEKMG EIVTDR LEE NFRELMNYDF TAQMENSLDQ VANHEAEWKA VLDHFFSDFT QQLDKAEKDP EEGGMRPNQM VLTSIDCPTC GRKMGIR TA STGVFLGCSG YALPPKERCK TTINLVPENE VLNVLEGEDA ETNALRAKRR CPKCGTAMDS YLIDPKRKLH VCGNNPTC D GYEIEEGEFR IKGYDGPIVE CEKCGSEMHL KMGRFGKYMA CTNEECKNTR KILRNGEVAP PKEDPVPLPE LPCEKSDAY FVLRDGAAGV FLAANTFPKS RETRAPLVEE LYRFRDRLPE KLRYLADAPQ QDPEGNKTMV RFSRKTKQQY VSSEKDGKAT GWSAFYVDG KWVEGKK

UniProtKB: DNA topoisomerase 1

Macromolecule #6: non-template DNA strand

• Macromolecule: Name: non-template DNA strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 15.422909 KDa

Sequence

String:

(DT)(DT)(DA)(DG)(DT)(DT)(DA)(DG)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DC)(DA)(DT)(DT)(DA) (DT)(DT)(DT)(DT)(DT)(DA)(DT)(DC)(DG) (DA)(DT)(DC)(DT)(DT)(DC)(DG)(DG)(DA)(DA) (DG) (DA)(DG)(DA)(DT)(DT)(DC)(DA)(DG) (DA)(DG)

Macromolecule #8: template DNA strand

• Macromolecule: Name: template DNA strand / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 15.212735 KDa

Sequence

String:

(DC)(DT)(DC)(DT)(DG)(DA)(DA)(DT)(DC)(DT) (DC)(DT)(DT)(DC)(DC)(DG)(DA)(DC)(DG)(DC) (DG)(DC)(DC)(DG)(DC)(DG)(DA)(DA)(DA) (DA)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)

Macromolecule #7: RNA

• Macromolecule: Name: RNA / type: rna / ID: 7 / Number of copies: 1
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 4.532764 KDa

Sequence

String:

GAGUCCGCGG CGCG

Macromolecule #9: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #10: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 10 / Number of copies: 5 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 10 mg/mL

Buffer

pH: 7.5
Component:

Concentration	Name
10.0 mM	HEPES/KOH
150.0 mM	potassium acetate
5.0 mM	magnesium acetate
0.01 mM	zinc chloride
2.0 mM	DTT

• Grid: Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 35 sec. / Pretreatment - Atmosphere: OTHER
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.9 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
• Sample stage: Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Software - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: NONE
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10189
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

Atomic model buiding 1

Initial model

PDB ID	Chain
6alh	source_name: PDB, initial_model_type: experimental model
4rul	source_name: PDB, initial_model_type: experimental model
3px7	source_name: PDB, initial_model_type: experimental model

• Details: Initial rigid body fit was done in UCSF chimera, followed by all-atom refinement of RNAP using Phenix and Coot, and flexible fitting of TopoI domains.
• Refinement: Space: REAL / Protocol: OTHER

Output model

PDB-9gdh:
RNAP-TopoI complex on long-overhang scaffold - orientation 2