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- EMDB-72792: RNA polymerase II on Super pause sequence in the sidetracked state -

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Basic information

Entry
Database: EMDB / ID: EMD-72792
TitleRNA polymerase II on Super pause sequence in the sidetracked state
Map data
Sample
  • Complex: RNA polymerase II paused elongation complex
    • Protein or peptide: x 12 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 2 types
KeywordsRNA polymerase II / Elongation complex / TRANSCRIPTION
Function / homology
Function and homology information


nuclear DNA-directed RNA polymerase complex / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex ...nuclear DNA-directed RNA polymerase complex / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / mRNA Splicing - Major Pathway / mRNA Polyadenylation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / DNA-directed RNA polymerase complex / transcription-coupled nucleotide-excision repair / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / fibrillar center / transcription by RNA polymerase II / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / nucleic acid binding / nuclear speck / protein dimerization activity / hydrolase activity / chromosome / nucleotide binding / RNA-directed RNA polymerase activity / nucleolus / DNA-templated transcription / DNA binding / metal ion binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon ...DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / Zinc finger, TFIIS-type / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / 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 Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / 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 polymerase Rpb1, domain 1 / 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, 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 / Armadillo-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / : / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein ...DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / : / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB9
Similarity search - Component
Biological speciesSus scrofa (pig) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsVazquez Nunez R / Vos SM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2-GM146254 United States
CitationJournal: To Be Published
Title: RNA polymerase II on Super pause sequence in the sidetracked state
Authors: Vazquez Nunez R / Vos SM
History
DepositionSep 20, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72792.png

Downloads & links

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Map

FileDownload / File: emd_72792.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0289
Minimum - Maximum-0.14287959 - 0.2640266
Average (Standard dev.)-0.0000615005 (±0.008118265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72792_msk_1.map
Projections & Slices
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Additional map: Unsharpened map

Fileemd_72792_additional_1.map
AnnotationUnsharpened map
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Half map: #2

Fileemd_72792_half_map_1.map
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Half map: #1

Fileemd_72792_half_map_2.map
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Sample components

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Entire : RNA polymerase II paused elongation complex

EntireName: RNA polymerase II paused elongation complex
Components
  • Complex: RNA polymerase II paused elongation complex
    • Protein or peptide: DNA-directed RNA polymerase subunit
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB4
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC1
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2
    • Protein or peptide: DNA-directed RNA polymerase subunit
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB11-a
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4
    • DNA: Non-template DNA strand
    • RNA: RNA
    • DNA: Template DNA strand
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RNA polymerase II paused elongation complex

SupramoleculeName: RNA polymerase II paused elongation complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15 / Details: Sidetracked RNA
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: DNA-directed RNA polymerase subunit

MacromoleculeName: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 166.849047 KDa
SequenceString: SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIEL AKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK RLTHVYDLCK GKNICEGGEE MDNKFGVEQP E GDEDLTKE ...String:
SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIEL AKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK RLTHVYDLCK GKNICEGGEE MDNKFGVEQP E GDEDLTKE KGHGGCGRYQ PRIRRSGLEL YAEWKHVNED SQEKKILLSP ERVHEIFKRI SDEECFVLGM EPRYARPEWM IV TVLPVPP LSVRPAVVMQ GSARNQDDLT HKLADIVKIN NQLRRNEQNG AAAHVIAEDV KLLQFHVATM VDNELPGLPR AMQ KSGRPL KSLKQRLKGK EGRVRGNLMG KRVDFSARTV ITPDPNLSID QVGVPRSIAA NMTFAEIVTP FNIDRLQELV RRGN SQYPG AKYIIRDNGD RIDLRFHPKP SDLHLQTGYK VERHMCDGDI VIFNRQPTLH KMSMMGHRVR ILPWSTFRLN LSVTT PYNA DFDGDEMNLH LPQSLETRAE IQELAMVPRM IVTPQSNRPV MGIVQDTLTA VRKFTKRDVF LERGEVMNLL MFLSTW DGK VPQPAILKPR PLWTGKQIFS LIIPGHINCI RTHSTHPDDE DSGPYKHISP GDTKVVVENG ELIMGILCKK SLGTSAG SL VHISYLEMGH DITRLFYSNI QTVINNWLLI EGHTIGIGDS IADSKTYQDI QNTIKKAKQD VIEVIEKAHN NELEPTPG N TLRQTFENQV NRILNDARDK TGSSAQKSLS EYNNFKSMVV SGAKGSKINI SQVIAVVGQQ NVEGKRIPFG FKHRTLPHF IKDDYGPESR GFVENSYLAG LTPTEFFFHA MGGREGLIDT AVKTAETGYI QRRLIKSMES VMVKYDATVR NSINQVVQLR YGEDGLAGE SVEFQNLATL KPSNKAFEKK FRFDYTNERA LRRTLQEDLV KDVLSNAHIQ NELEREFERM REDREVLRVI F PTGDSKVV LPCNLLRMIW NAQKIFHINP RLPSDLHPIK VVEGVKELSK KLVIVNGDDP LSRQAQENAT LLFNIHLRST LC SRRMAEE FRLSGEAFDW LLGEIESKFN QAIAHPGEMV GALAAQSLGE PATQMTLNTF HYAGVSAKNV TLGVPRLKEL INI SKKPKT PSLTVFLLGQ SARDAERAKD ILCRLEHTTL RKVTANTAIY YDPNPQSTVV AEDQEWVNVY YEMPDFDVAR ISPW LLRVE LDRKHMTDRK LTMEQIAEKI NAGFGDDLNC IFNDDNAEKL VLRIRIMNSD ENKMQEEEEV VDKMDDDVFL RCIES NMLT DMTLQGIEQI SKVYMHLPQT DNKKKIIITE DGEFKALQEW ILETDGVSLM RVLSEKDVDP VRTTSNDIVE IFTVLG IEA VRKALERELY HVISFDGSYV NYRHLALLCD TMTCRGHLMA ITRHGVNRQD TGPLMKCSFE ETVDVLMEAA AHGESDP MK GVSENIMLGQ LAPAGTGCFD LLLDAEKCKY GME

UniProtKB: DNA-directed RNA polymerase subunit

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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: Sus scrofa (pig)
Molecular weightTheoretical: 132.419828 KDa
SequenceString: DDEITPDLWQ EACWIVISSY FDEKGLVRQQ LDSFDEFIQM SVQRIVEDAP PIDLQAEAQH ASGEVEEPPR YLLKFEQIYL SKPTHWERD GAPSPMMPNE ARLRNLTYSA PLYVDITKTV IKEGEEQLQT QHQKTFIGKI PIMLRSTYCL LNGLTDRDLC E LNECPLDP ...String:
DDEITPDLWQ EACWIVISSY FDEKGLVRQQ LDSFDEFIQM SVQRIVEDAP PIDLQAEAQH ASGEVEEPPR YLLKFEQIYL SKPTHWERD GAPSPMMPNE ARLRNLTYSA PLYVDITKTV IKEGEEQLQT QHQKTFIGKI PIMLRSTYCL LNGLTDRDLC E LNECPLDP GGYFIINGSE KVLIAQEKMA TNTVYVFAKK DSKYAYTGEC RSCLENSSRP TSTIWVSMLA RGGQGAKKSA IG QRIVATL PYIKQEVPII IVFRALGFVS DRDILEHIIY DFEDPEMMEM VKPSLDEAFV IQEQNVALNF IGSRGAKPGV TKE KRIKYA KEVLQKEMLP HVGVSDFCET KKAYFLGYMV HRLLLAALGR RELDDRDHYG NKRLDLAGPL LAFLFRGMFK NLLK EVRIY AQKFIDRGKD FNLELAIKTR IISDGLKYSL ATGNWGDQKK AHQARAGVSQ VLNRLTFAST LSHLRRLNSP IGRDG KLAK PRQLHNTLWG MVCPAETPEG HAVGLVKNLA LMAYISVGSQ PSPILEFLEE WSMENLEEIS PAAIADATKI FVNGCW VGI HKDPEQLMNT LRKLRRQMDI IVSEVSMIRD IREREIRIYT DAGRICRPLL IVEKQKLLLK KRHIDQLKER EYNNYSW QD LVASGVVEYI DTLEEETVML AMTPDDLQEK EVAYCSTYTH CEIHPSMILG VCASIIPFPD HNQSPRNTYQ SAMGKQAM G VYITNFHVRM DTLAHVLYYP QKPLVTTRSM EYLRFRELPA GINSIVAIAS YTGYNQEDSV IMNRSAVDRG FFRSVFYRS YKEQESKKGF DQEEVFEKPT RETCQGMRHA IYDKLDDDGL IAPGVRVSGD DVIIGKTVTL PENEDELEGT NRRYTKRDCS TFLRTSETG IVDQVMVTLN QEGYKFCKIR VRSVRIPQIG DKFASRHGQK GTCGIQYRQE DMPFTCEGIT PDIIINPHAI P SRMTIGHL IECLQGKVSA NKGEIGDATP FNDAVNVQKI SNLLSDYGYH LRGNEVLYNG FTGRKITSQI FIGPTYYQRL KH MVDDKIH SRARGPIQIL NRQPMEGRSR DGGLRFGEME RDCQIAHGAA QFLRERLFEA SDPYQVHVCN LCGIMAIANT RTH TYECRG CRNKTQISLV RMPYACKLLF QELMSMSIAP RMMSV

UniProtKB: UNIPROTKB: A0A8D1CBC6

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Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 30.565066 KDa
SequenceString: PYANQPTVRI TELTDENVKF IIENTDLAVA NSIRRVFIAE VPIIAIDWVQ IDANSSVLHD EFIAHRLGLI PLTSDDIVDK LQYSRDCTC EEFCPECSVE FTLDVRCNED QTRHVTSRDL ISNSPRVIPV TSRNRDNDPS DYVEQDDILI VKLRKGQELR L RAYAKKGF ...String:
PYANQPTVRI TELTDENVKF IIENTDLAVA NSIRRVFIAE VPIIAIDWVQ IDANSSVLHD EFIAHRLGLI PLTSDDIVDK LQYSRDCTC EEFCPECSVE FTLDVRCNED QTRHVTSRDL ISNSPRVIPV TSRNRDNDPS DYVEQDDILI VKLRKGQELR L RAYAKKGF GKEHAKWNPT AGVAFEYDPD NALRHTVYPK PEEWPKSEYS ELDEDESQAP YDPNGKPERF YYNVESCGSL RP ETIVLSA LSGLKKKLSD LQTQLSHEIQ

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

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Macromolecule #4: DNA-directed RNA polymerase II subunit RPB4

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 14.981794 KDa
SequenceString:
EEDASQLIFP KEFETAETLL NSEVHMLLEH RKQQNESAED EQELSEVFMK TLNYTARFSR FKNRETIASV RSLLLQKKLH KFELACLAN LCPETAEESK ALIPSLEGRF EDEELQQILD DIQTKRSFQ

UniProtKB: DNA-directed RNA polymerase II subunit RPB4

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Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 24.38302 KDa
SequenceString: DDEEETYRLW KIRKTIMQLC HDRGYLVTQD GLDQTLEEFK AQFGGKPSEG RPRRTDLTVL VAHNDDPTDQ MFVFFPEEPK VGIKTIKVY CQRMQEENIT RALIVVQQGM TPSAKQSLVD MAPKYILEQF LQQELLINIT EHELVPEHVV MTKEEVTELL A RYKLRENQ ...String:
DDEEETYRLW KIRKTIMQLC HDRGYLVTQD GLDQTLEEFK AQFGGKPSEG RPRRTDLTVL VAHNDDPTDQ MFVFFPEEPK VGIKTIKVY CQRMQEENIT RALIVVQQGM TPSAKQSLVD MAPKYILEQF LQQELLINIT EHELVPEHVV MTKEEVTELL A RYKLRENQ LPRIQAGDPV ARYFGIKRGQ VVKIIRPSET AGRYITYRLV Q

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

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Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 8.978591 KDa
SequenceString:
KRITTPYMTK YERARVLGTR ALQIAMCAPV MVELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG VDELIISD

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

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Macromolecule #7: DNA-directed RNA polymerase subunit

MacromoleculeName: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 19.227205 KDa
SequenceString:
MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ PGRGFVLYPV KYKAIVFRPF KGEVVDAVV TQVNKVGLFT EIGPMSCFIS RHSIPSEMEF DPNSNPPCYK TMDEDIVIQQ DDEIRLKIVG TRVDKNDIFA I GSLMDDYL GLV

UniProtKB: DNA-directed RNA polymerase subunit

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Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 16.883902 KDa
SequenceString:
AGILFEDIFD VKDIDPEGKK FDRVSRLHCE SESFKMDLIL DVNIQIYPVD LGDKFRLVIA STLYEDGTLD DGEYNPTDDR PSRADQFEY VMYGKVYRIE GDETSTEAAT RLSAYVSYGG LLMRLQGDAN NLHGFEVDSR VYLLMKKLA

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

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Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.316925 KDa
SequenceString:
VGIRFCQECN NMLYPKEDKE NRILLYACRN CDYQQEADNS CIYVNKITHE VDELTQIIAD VSQDPTLPRT EDHPCQKCGH KEAVFFQSH SARAEDAMRL YYVCTAPHCG HRWTE

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

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Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 7.655123 KDa
SequenceString:
MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

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Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11-a

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB11-a / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.068013 KDa
SequenceString:
MNAPPAFESF LLFEGEKKIT INKDTKVPNA CLFTINKEDH TLGNIIKSQL LKDPQVLFAG YKVPHPLEHK IIIRVQTTPD YSPQEAFTN AITDLISELS LLEERFRVAI KDKQEG

UniProtKB: DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein

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Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 5.394418 KDa
SequenceString:
MIYICGECHT ENEIKSRDPI RCRECGYRIM YKKRTKRLVV FDAR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC4

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Macromolecule #13: Non-template DNA strand

MacromoleculeName: Non-template DNA strand / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.696502 KDa
SequenceString:
(DA)(DG)(DT)(DA)(DC)(DG)(DT)(DC)(DC)(DG) (DG)(DC)(DG)(DG)(DA)(DG)(DC)(DT)(DG)(DC) (DT)(DG)(DC)(DC)(DG)(DC)(DA)(DA)(DA) (DT)(DT)(DC)(DA)(DG)(DA)(DT)(DC)(DT)

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Macromolecule #15: Template DNA strand

MacromoleculeName: Template DNA strand / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.383296 KDa
SequenceString:
(DG)(DA)(DT)(DC)(DT)(DG)(DA)(DA)(DT)(DT) (DT)(DG)(DC)(DG)(DG)(DC)(DA)(DG)(DC)(DA) (DG)(DC)(DT)(DC)(DC)(DG)(DC)(DC)(DG) (DG)(DA)(DC)(DG)(DT)(DA)(DC)(DT)

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Macromolecule #14: RNA

MacromoleculeName: RNA / type: rna / ID: 14 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.108023 KDa
SequenceString:
UUUUGGCGGA GCUGCU

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Macromolecule #16: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 16 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #17: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 17 / 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 state2D array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.25 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 9160
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8a40


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9ycz:
RNA polymerase II on Super pause sequence in the sidetracked state

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